Description of Research
Fukunaga lab investigates the mechanism and biology of post-transcriptional gene regulation controlled by RNA-binding proteins and small silencing RNAs. Our research projects will answer fundamental biological questions and also potentially lead to therapeutic applications to human disease.
For the RNA-binding proteins projects, we are interested in novel post-transcriptional gene regulation mechanism performed by uncharacterized or poorly characterized RNA-binding proteins. We use Drosophila oogenesis and spermatogenesis as one of the model systems since post-transcriptional gene regulation is particularly important during these processes.
For the small silencing RNA projects, we are particularly interested in the mechanisms by which microRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced by Dicer enzymes and the mechanisms by the Dicer enzymes are regulated by Dicer-partner RNA-binding proteins. Specifically, we aim to understand the molecular mechanism by which the length of small silencing RNAs produced by Dicer is defined and regulated, which is a biologically significant question.
We use a combination of biochemistry, biophysics, Drosophila genetics, cell culture, and next-generation sequencing, in order to understand important biological questions from the atomic to the organismal level.
Lab Members
- Azali Azlan (postdoc)
- Yuki Taira (postdoc)
Publications
- Zhu L, Fukunaga R. RNA-binding protein Maca is crucial for gigantic male fertility factor gene expression, spermatogenesis, and male fertility, in Drosophila. PLoS Genetics. 17, e1009655, (2021)
- Vakrou S, Liu Y, Zhu L, Greenland GV, Simsek B, Hebl BV, Guan Y, Woldemichael K, Talbot CC, Aon MA, Fukunaga R, Abraham MR. Differences in molecular phenotype in mouse and human hypertrophic cardiomyopathy. Scientific Reports. 11, 13163, (2021)
- 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. Differences in microRNA-29 and Pro-fibrotic Gene Expression in Mouse and Human Hypertrophic Cardiomyopathy. Front Cardiovasc Med. 6,170, (2019)
- Zhu L, Liao ES, Fukunaga R. Drosophila Regnase-1 RNase is required for mRNA and miRNA profile remodelling during larva-to-adult metamorphosis. RNA Biology 16, 1386-1400, (2019)
- Zhu L, Liao ES, Ai Y, Fukunaga R. RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries. PLoS ONE 14, e0217603, (2019)
- Liao ES, Kandasamy SK, Zhu L, Fukunaga R. DEAD-box RNA helicase Belle post-transcriptionally promotes gene expression in an ATPase activity-dependent manner. RNA 25, 825-839, (2019)
- Zhu L, Kandasamy SK, Liao ES, Fukunaga R. LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes. Nature Communications, 9, 4031, (2018)
- Liao ES, Ai Y, Fukunaga R. An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in Drosophila testes. Heliyon, 4, e00706, (2018)
- 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. Allele-specific differences in transcriptome, miRNome, and mitochondrial function in two hypertrophic cardiomyopathy mouse models. JCI insight, 3, e94493, (2018)
- Fukunaga R. Dicer-2 partner protein Loquacious-PD allows hairpin RNA processing into siRNAs in the presence of inorganic phosphate. Biochemical and Biophysical Research Communications, 498, 1022–1027, (2018)
- Zhu L, Kandasamy SK, Fukunaga R. Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem. Nucleic Acids Res., 46, 3726-3741, (2018)
- Kandasamy SK, Zhu L, Fukunaga R. 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. RNA, 23, 1139-1153, (2017)
- Kandasamy SK, Fukunaga R. Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production. Proc. Natl. Acad. Sci. U S A. 113, 14031-14036, (2016)
- Lin X, Steinberg S, Kandasamy S, Afzal J, Mbiyangandu B, Liao ES, Guan Y, Corona-Villalobos C, Matkovich S, Epstein N, Tripodi D, Huo Z, Cutting G, Abraham T, Fukunaga R, Abraham R. Common MiR-590 Variant rs6971711 present only in African Americans reduces miR-590 biogenesis. PLoS ONE. 11, e0156065, (2016)
- Yanagisawa T, Ishii R, Hikida Y, Fukunaga R, Sengoku T, Sekine SI, Yokoyama S. A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNACys. J. Struct. Funct. Genomics. 16, 25-41, (2015)
- Fukunaga R, Colpan C, Han BW, Zamore PD. Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. EMBO Journal, 18, 371-384, (2014)
- Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell, 151, 533-546, (2012)
- Cenik ES, Fukunaga R, Lu G, Dutcher R, Wang Y, Tanaka Hall TM, Zamore PD. Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease. Mol. Cell, 42, 172-814, (2011)
- Naganuma M, Sekine SI, Fukunaga R, Yokoyama S. Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization. Proc. Natl. Acad. Sci., 106, 8489-8494, (2009)
- Fukunaga R, Doudna JA. dsRNA with 5¢ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants. EMBO J., 28, 545-555, (2009)
- Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N¢-(o-Azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chem. Biol., 15, 1187-1197, (2008)
- Fukunaga R, Harada Y, Hirao I, Yokoyama S. Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon. Biochem Biophys Res Commun., 372, 480-485, (2008)
- Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase. J. Mol. Biol., 378, 634-652, (2008)
- Fukunaga R, Yokoyama S. Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus. J. Mol. Biol., 370, 128-141, (2007)
- Fukunaga R, Yokoyama S. The C-terminal domain of the archaeal leucyl-tRNA synthetase prevents misediting of isoleucyl-tRNAIle. Biochemistry, 46, 4985-4996, (2007)
- Fukunaga R, Yokoyama S. Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Nat. Struct. Mol. Biol., 14, 272-279, (2007)
- Fukunaga R, Yokoyama S. Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus. Acta Crystallogr. F, 63, 224-228, (2007)
- Fukunaga R, Yokoyama S. Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii. Acta Crystallogr. D, 63, 390-400, (2007)
- Yanagisawa T, Ishii R, Fukunaga R, Nureki O, Yokoyama S. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the Methanogenic archaeon Methanosarcina mazei. Acta Crystallogr. F, 62, 1031-1033, (2006)
- Sasaki H, Sekine S, Sengoku T, Fukunaga R, Hattori M, Utsunomiya Y, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S. Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase. Proc. Natl. Acad. Sci. 103, 14744-14749, (2006)
- Fukunaga R, Yokoyama S. Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase. J. Mol. Biol. 359, 901-912, (2006)
- Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Sekine S, Shirouzu M, Yokoyama S. Crystal structure of tRNA adenosine deaminase TadA from Aquifex aeolicus. J. Biol. Chem., 280, 16002-16008, (2005)
- Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S. The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nat. Struct. Mol. Biol. 12, 923-930, (2005)
- Fukunaga R, Yokoyama S. Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator base recognition for 3¢-end relocation toward the editing domain. Nat. Struct. Mol. Biol. 12, 915-922, (2005)
- Fukunaga R, Yokoyama S. Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain. J. Biol. Chem. 280, 29937-29945, (2005)
- Fukunaga R, Ishitani R, Nureki O, Yokoyama S. Crystallization of Leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii. Acta Crystallogr. F, 61, 30-32, (2005).
- Fukunaga R, Yokoyama S. Crystal Structure of Leucyl-tRNA Synthetase from the Archaeon Pyrococcus horikoshii Reveals a novel editing domain orientation. J. Mol. Biol. 346, 57-71, (2005).
- Fukunaga R, Yokoyama S. Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii. Acta Crystallogr. D, 60, 1916-1918, (2004)
- Fukunaga R, Yokoyama S. 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. Acta Crystallogr. D, 60, 1900-1902, (2004)
- Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S. Crystal Structures of the CP1 Domain from Thermus thermophilus Isoleucyl-tRNA synthetase and Its Complex with L-Valine. J. Biol. Chem. 279, 8396-8402, (2004)