RNA Molecular Medicine

Publication

2019-

Wan Yun Ho, Li-Ling Chak, Jin-Hui Hor, Fujia Liu, Sandra Diaz-Garcia, Jer-Cherng Chang, Emma Sanford, Maria J. Rodriguez, Durgadevi Alagappan, Su Min Lim, Yik-Lam Cho, Yuji Shimizu, Alfred Xuyang Sun, Sheue-Houy Tyan, Edward Koo, Seung Hyun Kim, John Ravits, Shi-Yan Ng, Katsutomo Okamura, Shuo-Chien Ling. (2023) FUS-dependent microRNA deregulations identity TRIB2 as a druggable target for ALS motor neurons. iScience, 26(11).
Feng, C., Torimaru, K., Lim, M. Y. T., Chak, L. L., Shiimori, M., Tsuji, K., Tanaka, T., Iida, J., and Okamura, K. (2023). A novel eukaryotic RdRP-dependent small RNA pathway represses antiviral immunity by controlling an ERK pathway component in the black-legged tick. PloS one. Mar 30;18(3).
Sook Yoong Chia, Ashwati Vipin, Kok Pin Ng, Haitao Tu, Ananth Bommakanti, Brian Zhiyang Wang, Yi Jayne Tan, Fatin Zahra Zailan, Adeline Su Lyn Ng, Shuo-Chien Ling, Katsutomo Okamura, Eng-King Tan, Nagaendran Kandiah, and Li Zeng. (2022) Upregulated Blood miR-150-5p in Alzheimer's Disease Dementia Is Associated with Cognition, Cerebrospinal Fluid Amyloid-β, and Cerebral Atrophy. J Alzheimers Dis. 88(4):1567-1584.
Alan A. L. Ong, Desiree-Faye Kaixin Toh, Manchugondanahalli S. Krishna, Kiran M. Patil, Katsutomo Okamura and Gang Chen. (2019) Incorporating 2-Thiouracil into Short Double-Stranded RNA-Binding Peptide Nucleic Acids for Enhanced Recognition of A-U Pairs and for Targeting a MicroRNA Hairpin Precursor. Biochemistry. 58(32):3444-3453
Goh E, Okamura K. (2019) Hidden sequence specificity in loading of single-stranded RNAs onto Drosophila Argonautes. Nucleic Acids Res. Apr 8;47(6):3101-3116.
Ong AAL, Toh DK, Patil KM, Meng Z, Yuan Z, Krishna MS, Devi G, Haruehanroengra P, Lu Y, Xia K, Okamura K, Sheng J, Chen G. (2019) General Recognition of U-G, U-A, and C-G Pairs by Double-Stranded RNA-Binding PNAs Incorporated with an Artificial Nucleobase. Biochemistry. Mar 12;58(10):1319-1331.

2012-2018

Li Zhou*, Mandy Y.T. Lim*, Prameet Kaur, Abil Saj, Diane Bortolamiol-Becet, Vikneswaran Gopal, Nicholas Tolwinski, Greg Tucker-Kellogg and Katsutomo Okamura (2018) Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development. eLife 7:e38389
Ryan Y.W. Teo* , Amit Anand*†, Vishweshwaren Sridhar, Katsutomo Okamura and Toshie Kai† (2018) Heterochromatin protein 1a functions for piRNA biogenesis predominantly from pericentric and telomeric regions in Drosophila. Nature Communications. 9(1):1735. (*: Co-first authors, †: co-corresponding authors)
Eling Goh and Katsutomo Okamura (2018) Gateway to Understanding Argonaute Loading of Single-Stranded RNAs: Preparation of Deep Sequencing Libraries with In Vitro Loading Samples. Methods Mol Biol. 1680:41-63
Mandy Y.T. Lim*, Alvin Wei Tian Ng*, Yuting Chou, Teck Por Lim, Amanda Simcox, Greg Tucker-Kellogg and Katsutomo Okamura (2016) The Drosophila Dicer-1 partner Loquacious enhances miRNA processing from hairpins with unstable structures at the dicing site. Cell Reports 15 (8) 1795–1808 (*: Co-first authors)
Diane Bortolamiol-Becet, Fuqu Hu, David Jee, Jiayu Wen, Katsutomo Okamura, Ching-Jung Lin, Stefan L. Ameres and Eric C. Lai (2015) Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor. Molecular Cell 59(2): 217–228
Li-Ling Chak, Jaaved Mohammed, Eric C. Lai, Greg Tucker-Kellogg and Katsutomo Okamura (2015) A deeply conserved, non-canonical miRNA hosted by ribosomal DNA. RNA 21(3): 375-384
Jiayu Wen, Hong Duan, Fernando Bejarano, Katsutomo Okamura, Lacramioara Fabian, Julie A. Brill, Diane Bortolamiol-Becet, Raquel Martin, J. Graham Ruby, and Eric C. Lai (2014) Adaptive regulation of testis gene expression and control of male fertility by the Drosophila hairpin RNA pathway. Molecular Cell 57(1):165-178
Jiayu Wen, Jaaved Mohammed, Diane Bortolamiol-Becet, Harrison Tsai, Nicolas Robine, Jakub O. Westholm, Erik Ladewig, Qi Dai, Katsutomo Okamura, Alex S. Flynt, Dayu Zhang, Justen Andrews, Lucy Cherbas, Thomas C Kaufman, Peter Cherbas, Adam Siepel, Eric C. Lai (2014) Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines. Genome Research 24(7):1236-50.
Katsutomo Okamura*, Erik Ladewig, Li Zhou and Eric C. Lai* (2013) Functional small RNAs are generated from select miRNA hairpin loops in flies and mammals. Genes & Development 27(7):778-92 (*: co-corresponding authors)
Erik Ladewig, Katsutomo Okamura, Alex S. Flynt, Jakub O. Westholm and Eric C. Lai (2012) Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Research 22(9):1634-45
Jakub O. Westholm, Erik Ladewig, Katsutomo Okamura, Nicolas Robine and Eric C. Lai (2012) Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. RNA 18(2):177-92

2000-2011

Katsutomo Okamura, Nicolas Robine, Ying Liu, Qinghua Liu, and Eric C. Lai (2011) R2D2 organizes small regulatory RNA pathways in Drosophila. Mol. Cell. Biol. 31(4):884-96
Wei-Jen Chung, Phaedra Agius, Jakub O. Westholm, Michael Chen, Katsutomo Okamura, Nicolas Robine, Christina S. Leslie, and Eric C. Lai (2011) Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans Genome Research 21(2):286-300
Eugene Berezikov, Nicolas Robine, Anastasia Samsonova, Jakub O. Westholm, Ammar Naqvi, Jui-Hung Hung, Katsutomo Okamura, Qi Dai, Raquel Martin, Yongjun Zhao, Phillip D. Zamore, Gregory J. Hannon, Marco A. Marra, Zhiping Weng, Norbert Perrimon, and Eric C. Lai (2011), Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research 21(2):203-15
Daniel Hain, Brian R. Bettencourt, Katsutomo Okamura, Tibor Csorba, Wibke Meyer, Zhigang Jin, Jason Biggerstaff, Haruhiko Siomi, Gyorgy Hutvagner, Eric C. Lai, Michael Welte, H.-Arno J. Müller. (2010) Natural variation of the amino-terminal glutamine-rich domain in Drosophila argonaute2 is not associated with developmental defects. PLoS One 5(12):e15264.
The modENCODE consortium et al. (40th in 96 authors) (2010) Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE, Science 330(6012):1787-97
Nicolas Robine, Nelson C. Lau, Sudha Balla, Zhigang Jin, Katsutomo Okamura, Satomi Kuramochi-Miyagawa, Michael D. Blower, Eric C. Lai. (2009) A Broadly Conserved Pathway Generates 3'UTR-Directed Primary piRNAs. Current Biology. 19(24): 2066-2076.
Katsutomo Okamura, Na Liu and Eric C. Lai (2009) Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Molecular Cell. 36(3): 431-44.
Katsutomo Okamura*, Sudha Balla*, Raquel Martin, Na Liu and Eric C. Lai (2008) Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Droophila. Nature Structural and Molecular Biology 15(6): 581-90 (*: Equal contribution)
Wei-Jen Chung*, Katsutomo Okamura*, Raquel Martin* and Eric C. Lai (2008) Endogenous RNA interference provides a somatic defense against Drosophila transposons. Current Biology 18(11): 795-802. (*: Equal contribution)
Katsutomo Okamura, Wei-Jen Chung, J. Graham Ruby, Huili Guo, David P. Bartel and Eric C. Lai (2008) The Drosophila hairpin RNA pathway generates endogenous siRNAs Nature 453(7196): 803-6
Katsutomo Okamura, Michael D. Phillips, David M. Tyler, Hong Duan, Yu-ting Chou and Eric C. Lai (2008) The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nature Structural and Molecular Biology 15(4): 354-63
Pelin Cayirlioglu, Ilona Grunwald Kadow, Xiaoli Zhan, Katsutomo Okamura, Greg S.B. Suh, Dorian Gunning, Eric C. Lai, David J. Anderson and S. Lawrence Zipursky (2008) Hybrid Neurons In a microRNA Mutant Are Putative Evolutionary Intermediates In Insect CO2 Sensory Systems. Science 319(5867): 1256-60
David M. Tyler, Katsutomo Okamura, Wei-jen Chung, Joshua W. Hagen, Eugene Berezikov, Gregory J. Hannon, and Eric C. Lai (2008) Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes & Development 22(1): 26-36.
Serena J. Silver, Joshua W. Hagen, Katsutomo Okamura, Norbert Perrimon and Eric C. Lai (2007) Functional screening identifies miR-315 as a potent activator of Wingless signaling. Proc Natl Acad Sci U S A. 104(46): 18151-6
Katsutomo Okamura, Joshua W. Hagen, Hong Duan, David M. Tyler and Eric C. Lai (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130(1): 89-100
Katsutomo Okamura, Akira Ishizuka, Haruhiko Siomi and Mikiko C. Siomi (2004) Distinct roles for Drosophila Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes & Development 18, 1655-1666
Katsutomo Okamura, Yukio Kimata, Hironori Higashio, Akio Tsuru, and Kenji Kohno (2000) Dissociation of Kar2/BiP from an ER sensory molecule, Ire1p, triggers the unfolded protein response in yeast. Biochemical and Biophysical Research Communications 279, 445-450

Review Articles

Mandy Y-.T-. Lim, Katsutomo Okamura (2017) Switches in Dicer Activity During Oogenesis and Early Development. Results Probl Cell Differ. (63):325-351
Jun Wei Pek* and Katsutomo Okamura* (2015) Regulatory RNAs discovered in unexpected places. WIREs RNA (6):671-86 (*: co-corresponding authors)
Fuqu Hu Eric C. Lai and Katsutomo Okamura (2014) A Signaling-Induced Switch in Dicer Localization and Function. Developmental Cell 31(5):523-4
Li-Ling Chak and Katsutomo Okamura (2014) Argonaute-dependent small RNAs derived from single-stranded non-structured precursors. Frontiers in Genetics 5: 172.
Katsutomo Okamura (2013) Argonaute reformatting Molecular Cell 50(3):305-6
Katsutomo Okamura (2011) Diversity of animal small RNA pathways and their biological utility WIREs RNA DOI: 10.1002/wrna.113
Katsutomo Okamura and Eric C. Lai (2010) A deathly DNase activity for dicer. Developmental Cell 18;18(5):692-4.
Katsutomo Okamura, Wei-Jen Chung, Eric C Lai (2008) The long and short of inverted repeat genes in animals: microRNAs, mirtrons and hairpin RNAs. Cell Cycle 15; 7(18): 2840-5.
Katsutomo Okamura, Eric C Lai. (2008) Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol. 9(9): 673-8.
Na Liu, Katsutomo Okamura, David M Tyler, Michael D Phillips, Wei-Jen Chung, Eric C Lai (2008) The evolution and functional diversification of animal microRNA genes. Cell Res. 18(10): 985-96.