Publications

Independent position at OSU

Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module.
Li YC, Chao TC, Kim HJ, Cholko T, Chen SF, Li G, Snyder L, Nakanishi K, Chang C, Murakami K, Garcia BA, Boyer TG, Tsai KL.
Science Advances, 7: eabd4484 (2021)

Human Argonaute2 and Argoanute3 are catalytically activated by different lengths of guide RNA
Park MS, Sim GY, Kehling AC, & Nakanishi K.
Proc Natl Acad Sci U S A., 117, 28576-28578 (2020)
bioRxiv

Multidomain Convergence of Argonaute during RISC Assembly Correlates with the Formation of Internal Water Clusters
Park MS, Araya-Secchi R, Brackbill JA, Phan HD, Kehling AC, Abd El-Wahab EW, Dayeh DM, Sotomayor M. & Nakanishi K.
Molecular Cell, 75, 725-740 (2019)

Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA
Dayeh DM, William AC, Kitzrow K, Musier-Forsyth K. & Nakanishi K.
Nucleic Acids Research,  gky496, https://doi.org/10.1093/nar/gky496 (2018)

Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA target cleavage
Dayeh DM, Kruithoff BC. & Nakanishi K.
Journal of Biological Chemistry, 293, 6308-6325 (2018) 

Human Argonaute3 has slicer activity
Park MS, Phan HD, Busch F, Hinckley SH, Brackbill JA, Wysocki VH. & Nakanishi K.
Nucleic Acids Research, 45, 11867-11877 (2017)

Quantification of miRNAs Co-Immunoprecipitated with Argonaute Proteins Using SYBR Green-Based qRT-PCR
Phan HD, Li J, Poi M. & Nakanishi K.
Methods in Molecular Biology 1680, Published Online (2017)

Cloning and Identification of Recombinant Argonaute-Bound Small RNAs Using Next-Generation Sequencing
Gangras P, Dayeh DM, Mabin JW, Nakanishi K. & Singh G.
Methods in Molecular Biology 1680, Published Online (2017)

Conformational and chemical selection by a trans-acting editing domain
Danhart EM, Bakhtina M, Cantara WA, Kuzmishin AB, Ma X, Sanford BL, Košutić M, Goto Y, Suga H, Nakanishi K, Micura R, Foster MP. & Musier-Forsyth K.
Proc Natl Acad Sci U S A. 114, (33) E6774-E6783 (2017)

GW182-free microRNA silencing complex controls post-transcriptional gene expression during Caenorhabditis elegans embryogenesis
Jannot G, Michaud P, Huberdeau MQ, Morel-Berryman L, Brackbill JA, Piquet S, McJunkin K, Nakanishi K. & Simard MJ.
PLOS Genetics 12, (12):e1006484ine (2016)

ERK Activation Globally Downregulates miRNAs through Phosphorylating Exportin-5
Sun HL, Cui R, Zhou J, Teng KY, Hsiao YH, Nakanishi K, Fassan M, Luo Z, Shi G, Tili E, Kutay H, Lovat F, Vicentini C, Huang HL, Wang SW, Kim T, Zanesi N, Jeon YJ, Lee TJ, Guh JH, Hung MC, Ghoshal K, Teng CM, Peng Y. & Croce CM.
Cancer Cell 14, 723-736 (2016).

Anatomy of RISC: How do small RNAs and chaperones activate Argonaute proteins?
Nakanishi K.
Wiley Interdiscip. Rev. RNA. 7, 637-60 (2016).

The evolutionary journey of Argonaute proteins.
Swarts DC, Makarova K, Wang Y, Nakanishi K, Ketting RF, Koonin EV, Patel DJ. & Oost J. van der.
Nat. Struct. Mol. Biol. 21, 931-932 (2014).

 

Postdoctroral and graduate publications
Eukaryote-Specific Insertion Elements Control Human ARGONAUTE Slicer Activity.
Nakanishi K, Ascano M, Gogakos T, Ishibe-Murakami S, Serganov AA, Briskin D, Morozov P, Tuschl T. & Patel DJ.
Cell Rep. 3, 1893-1900 (2013).

EGFR Modulates miRNA Maturation in Response to Hypoxia through Phosphorylation of Ago2.
Shen J, Xia W, Khotskaya YB, Huo L, Nakanishi K, Lim SO, Du Y, Wang Y, Chang WC, Chen CH, Hsu JL, Lam YC, James BP, Liu CG, Liu X, Patel DJ. & Hung MC.
Nature 497, 383-387 (2013).

Structure of yeast Argonaute with guide RNA.
Nakanishi K, Weinberg DE, Bartel DP. & Patel DJ.
Nature 486, 368-374 (2012).

The inside-out mechanism of Dicers from budding yeasts.
Weinberg DE, Nakanishi K, Patel DJ. & Bartel DP.
Cell 146, 262-276 (2011).

Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.
Nakanishi K, Bonnefond L, Kimura S, Suzuki T, Ishitani R. & Nureki O.
Nature 461, 1144-1148 (2009).

Structural basis for anticodon recognition by methionyl-tRNA synthetase.
Nakanishi K, Ogiso Y, Nakama T, Fukai S. & Nureki O.
Nat. Struct. Mol. Biol. 12, 931-932 (2005).

Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain.
Nakanishi K, Fukai S, Ikeuchi Y, Soma A, Sekine Y, Suzuki T, & Nureki O.
Proc. Natl. Acad. Sci. U. S. A. 24, 7487-7492 (2005).

Recent progress of structural biology of tRNA processing and modification.
Nakanishi K. & Nureki O.
Mol. Cells 19, 157-166 (2005).

Relation between tRNase activity and the structure of colicin D according to X-ray crystallography.
Yajima S, Nakanishi K, Takahashi K, Ogawa T, Hidaka M, Kezuka Y, Nonaka T, Ohsawa K. & Masaki H.
Biochem. Biophys. Res. Commun. 24, 966-973 (2004).

 

BOOKS

Argonaute proteins -Methods and Protocols- 
(Springer)
Editors: Katsutomo Okamura and Kotaro Nakanishi