Fukunaga Lab
Johns Hopkins University School of Medicine
Department of Biological Chemistry
Studying RNA-binding proteins and small silencing RNAs
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Publications
42. RNA-binding protein Maca is crucial for gigantic male fertility factor gene expression, spermatogenesis, and male fertility, in Drosophila
Zhu L, Fukunaga R
PLoS Genetics. 17(6): e1009655. (2021)
41. Differences in molecular phenotype in mouse and human hypertrophic cardiomyopathy
Vakrou S, Liu Y, Zhu L, Greenland GV, Simsek B, Hebl VB, Guan Y, Woldemichael K, Talbot CC Jr, Aon MA, Fukunaga R, Abraham MR
Scientific Reports. 11: 13163 (2021)
40. Differences in microRNA-29 and Pro-fibrotic Gene Expression in Mouse and Human Hypertrophic Cardiomyopathy
Liu Y, Afzal J, Vakrou S, Greenland GV, Talbot CC Jr, Hebl VB, Guan Y, Karmali R, Tardiff JC, Leinwand LA, Olgin JE, Das S, Fukunaga R, Abraham MR
Frontiers in Cardiovascular Medicine. 6:170. (2019)
39. Drosophila Regnase-1 RNase is required for mRNA and miRNA profile remodeling during larva-to-adult metamorphosis
Zhu L, Liao ES, Fukunaga R
RNA Biology. 16(10):1386-1400. (2019)
38. RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries
Zhu L, Liao ES, Ai Y, Fukunaga R
PLOS ONE. 14(5): e0217603 (2019)
37. DEAD-box RNA helicase Belle post-transcriptionally promotes gene expression in an ATPase activity-dependent manner
Liao ES, Kandasamy SK, Zhu L, Fukunaga R
RNA. 25: 825-839 (2019)
36. LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes
Zhu L, Kandasamy SK, Liao ES, Fukunaga R
Nature Communications. 9(1):4031 (2018)
35. An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in Drosophila testes
Liao ES, Ai Y, Fukunaga R
Heliyon. 4 e00706 (2018)
34. Allele-specific differences in transcriptome, miRNome, and mitochondrial function in two hypertrophic cardiomyopathy mouse models
Vakrou S, Fukunaga R, Foster DB, Sorensen L, Liu Y, Guan Y, Woldemichael K, Pineda-Reyes R, Liu T, Jill C. Tardiff JC, Leinwand LA, Tocchetti CG, Abraham TP, Brian O’Rourke B, Aon MA, Abraham MR
JCI Insight. 3(6): e94493 (2018)
33. Dicer-2 partner protein Loquacious-PD allows hairpin RNA processing into siRNAs in the presence of inorganic phosphate
Fukunaga R.
Biochemical and Biophysical Research Communications. 498: 1022–1027 (2018)
32. Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem
Zhu L, Kandasamy SK, Fukunaga R.
Nucleic Acid Research. 46, 3726-3741, (2018)
31. Kinetic Analysis of Small Silencing RNA Production by Human and Drosophila Dicer Enzymes In Vitro.
Liao SE, Fukunaga R.
Methods Mol Biol. 1680:101-121 (2018)
30. The C-terminal dsRNA-binding domain of Drosophila Dicer-2 is crucial for efficient and high-fidelity production of siRNA and loading of siRNA to Argonaute2
Kandasamy SK, Zhu L, Fukunaga R
RNA, 23, 1139-1153, (2017)
29. Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production
Kandasamy SK, Fukunaga R.
Proc. Natl. Acad. Sci. U S A. 113(49):14031-14036, (2016)
28. Common MiR-590 Variant rs6971711 present only in African Americans reduces miR-590 biogenesis
Lin X*, Steinberg S, Kandasamy S, Afzal J, Mbiyangandu B, Liao S, Guan Y, Corona-Villalobos C, Matkovich S, Epstein N, Tripodi D, Huo Z, Cutting G, Abraham T, Fukunaga R, Abraham R
PLoS ONE. 11(5): e0156065. (2016)
27. A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNACys
Yanagisawa T, Ishii R, Hikida Y, Fukunaga R, Sengoku T, Sekine SI, Yokoyama S,
J. Struct. Funct. Genomics. 16, 25-41, (2015)
26. A universal small molecule, inorganic phosphate, restricts the substrate specificity of Dicer-2 in small RNA biogenesis
Fukunaga R, Zamore PD
Cell Cycle. 13(11):1671-6. (2014)
25. Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain
Fukunaga R, Colpan C, Han BW, Zamore PD,
EMBO Journal, 18, 371-84, (2014)
Before 2013 (Fukunaga lab started in 2013)
24. Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals
Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD
Cell, 151, 533-46, (2012)
23. Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease
Cenik ES, Fukunaga R, Lu G, Dutcher R, Wang Y, Tanaka Hall TM, Zamore PD
Mol. Cell, 42, 172-84, (2011)
22. Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization
Naganuma M, Sekine SI, Fukunaga R, Yokoyama S
Proc. Natl. Acad. Sci., 106, 8489-94, (2009)
21. dsRNA with 5¢ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants
Fukunaga R, Doudna JA,
EMBO J., 28, 545-55, (2009)
20. Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode Ne-(o-Azidobenzyloxycarbonyl) lysine for site-specific protein modification
Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S
Chem. Biol., 15, 1187-97, (2008)
19. Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon
Fukunaga R, Harada Y, Hirao I, Yokoyama S
Biochem Biophys Res Commun., 1, 372, 480-5, (2008)
18. Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase
Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S
J. Mol. Biol., 2, 378, 634-52, (2008)
17. Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus
Fukunaga R, Yokoyama S
J. Mol. Biol., 29, 370, 128-41, (2007)
16. The C-terminal domain of the archaeal leucyl-tRNA synthetase prevents misediting of isoleucyl-tRNAIle
Fukunaga R, Yokoyama S
Biochemistry, 1, 46, 4985-96, (2007)
15. Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Structural basis of phosphoserine ligation to tRNA for genetic code evolution
Fukunaga R, Yokoyama S
Nat. Struct. Mol. Biol., 14, 272-9, (2007)
14. Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus
Fukunaga R, Yokoyama S
Acta Crystallogr. F, 63, 224-8, (2007)
13. Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii
Fukunaga R, Yokoyama S
Acta Crystallogr. D, 63, 390-400, (2007)
12. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the Methanogenic archaeon Methanosarcina mazei
Yanagisawa T, Ishii R, Fukunaga R, Nureki O, Yokoyama S
Acta Crystallogr. F, 62, 1031-3, (2006)
11. Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase
Sasaki H, Sekine S, Sengoku T, Fukunaga R, Hattori M, Utsunomiya Y, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S
Proc. Natl. Acad. Sci. 103, 14744-9, (2006)
10. Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase
Fukunaga R, Yokoyama S
J. Mol. Biol. 359, 901-12, (2006)
9. Crystal structure of tRNA adenosine deaminase TadA from Aquifex aeolicus
Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Sekine S, Shirouzu M, Yokoyama S
J. Biol. Chem., 280, 16002-16008, (2005)
8. The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation
Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S
Nat. Struct. Mol. Biol. 12, 923-930, (2005)
7. Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator base recognition for 3¢-end relocation toward the editing domain
Fukunaga R, Yokoyama S
Nat. Struct. Mol. Biol. 12, 915-922, (2005)
6. Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain
Fukunaga R, Yokoyama S
J. Biol. Chem. 280, 29937-29945, (2005)
5. Crystallization of Leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii
Fukunaga R, Ishitani R, Nureki O, Yokoyama S
Acta Crystallogr. F, 61, 30-32, (2005).
4. Crystal Structure of Leucyl-tRNA Synthetase from the Archaeon Pyrococcus horikoshii Reveals a novel editing domain orientation
Fukunaga R, Yokoyama S
J. Mol. Biol. 346, 57-71, (2005).
3. Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii
Fukunaga R, Yokoyama S
Acta Crystallogr. D, 60, 1916-1918, (2004)
2. Crystallization and preliminary X-ray crystallographic study of the editing domain of Thermus thermophilus isoleucyl-tRNA synthetase complexed with pre- and post-transfer editing-substrate analogues
Fukunaga R, Yokoyama S
Acta Crystallogr. D, 60, 1900-1902, (2004)
1. Crystal Structures of the CP1 Domain from Thermus thermophilus Isoleucyl-tRNA synthetase and Its Complex with l-Valine
Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S
J. Biol. Chem. 279, 8396-8402, (2004)