2020
Littleton, E.S., Childress, M.L., Gosting, M.L., Jackson, A.N., Kojima, S. Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output. Sci. Rep.,10:21839
https://rdcu.be/ccaSp
Unruh BA, Kojima S. (2020) The Making and Breaking of RNAs: Dynamics of Rhythmic RNA Expression in mammals. J. Biol. Rhythms. 35 (6): 519-529
https://pubmed.ncbi.nlm.nih.gov/32965157/
Mosig, R.A., Castaneda, A.N., Deslauriers, J.C., Frazier, L.P., He, K.L., Maghzian, N., Pokharel, A., Schrier, C.T., Zhu, L., Koike, N., Tyson, J.J., Green, C.B., Takahashi, J.S., Kojima, S. Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the murine circadian clock.
https://www.biorxiv.org/content/10.1101/2020.07.27.222760v1
Yao, X, Kojima, S., and Chen, J. (2020) Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression. PLoS Comput. Biol. 16(4):e1007842.
https://www.ncbi.nlm.nih.gov/pubmed/32339166
Mosig, R.A. and Kojima, S. To code or not to code? That is the question for RNA in timekeeping. Biochem (Lond) 42 (2): BIO04202005.
https://doi.org/10.1042/BIO04202005
https://rdcu.be/ccaSp
Unruh BA, Kojima S. (2020) The Making and Breaking of RNAs: Dynamics of Rhythmic RNA Expression in mammals. J. Biol. Rhythms. 35 (6): 519-529
https://pubmed.ncbi.nlm.nih.gov/32965157/
Mosig, R.A., Castaneda, A.N., Deslauriers, J.C., Frazier, L.P., He, K.L., Maghzian, N., Pokharel, A., Schrier, C.T., Zhu, L., Koike, N., Tyson, J.J., Green, C.B., Takahashi, J.S., Kojima, S. Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the murine circadian clock.
https://www.biorxiv.org/content/10.1101/2020.07.27.222760v1
Yao, X, Kojima, S., and Chen, J. (2020) Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression. PLoS Comput. Biol. 16(4):e1007842.
https://www.ncbi.nlm.nih.gov/pubmed/32339166
Mosig, R.A. and Kojima, S. To code or not to code? That is the question for RNA in timekeeping. Biochem (Lond) 42 (2): BIO04202005.
https://doi.org/10.1042/BIO04202005
2019
Kojima, S. and Cimini D. (2019) Aneuploidy and gene expression: Is there dosage compensation? Epigenomics. 11(16): 1827-1837.
https://www.ncbi.nlm.nih.gov/pubmed/31755744
https://www.ncbi.nlm.nih.gov/pubmed/31755744
2018
Gendreau K.L*., Unruh, B.A*., Zhou, C., and Kojima. S. (2018) Identification and Characterization of Transcripts Regulated by Circadian Alternative Polyadenylation in Mouse Liver. G3: Genes, Genomes, Genetics. 8 (11), 3539-3548.
www.ncbi.nlm.nih.gov/pubmed/30181259
Kojima, S. (2018) “徒然独立日記〜黎明編〜” Japanese Society for Chronobiology Magazine 24 (1), 59-65. (Japanese)
http://chronobiology.jp/journal/JSC2018-1-059.pdf
Battogtokh D., Kojima, S., Tyson, J.J., (2018) Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network. PLoS Comput. Biol., 14 (2), e1005967
www.ncbi.nlm.nih.gov/pubmed/29447160
2017
Yoo, S-H, Kojima, S., Shimomura, K., Koike, N., Buhr, E., Furukawa, T., Ko, C.H., Gloston, G., Ayoub, C., Nohara, K., Reyes, B.A., Tsuchiya, Y., Yoo, O-J., Yagita, K., Lee, C., Chen, Z., Yamazaki, S., Green, C.B., Takahashi, J.S. (2017) Period2 3'-UTR and microRNA-24 regulate circadian rhythms by repressing PERIOD2 protein accumulation. Proc. Natl. Acad. Sci. USA, 114 (42), E8855-E8864.
https://www.ncbi.nlm.nih.gov/pubmed/28973913
https://www.ncbi.nlm.nih.gov/pubmed/28973913
2015
Kojima, S., Gendreau, K.L., Sher-Chen, E.L., Gao, P., and Green, C.B. (2015) Changes in poly(A) tail length dynamics from the loss of the circadian deadenylase, Nocturnin. Sci. Rep., 5: 17059
https://www.ncbi.nlm.nih.gov/pubmed/26586468
Kojima, S., and Green, C.B. (2015) Analysis of Circadian Regulation of Poly(A)-Tail Length. Methods in Enzymology 551:387-403
www.ncbi.nlm.nih.gov/pubmed/25662466
Kojima, S., and Green, C.B. (2015) Circadian genomics reveals a role for post-transcriptional regulation in mammals. Biochemistry 54(2):124-133.
www.ncbi.nlm.nih.gov/pubmed/25303020
https://www.ncbi.nlm.nih.gov/pubmed/26586468
Kojima, S., and Green, C.B. (2015) Analysis of Circadian Regulation of Poly(A)-Tail Length. Methods in Enzymology 551:387-403
www.ncbi.nlm.nih.gov/pubmed/25662466
Kojima, S., and Green, C.B. (2015) Circadian genomics reveals a role for post-transcriptional regulation in mammals. Biochemistry 54(2):124-133.
www.ncbi.nlm.nih.gov/pubmed/25303020
Before 2015
Kojima, S. (2014) Circadian rhythms and post-transcriptional gene regulatory mechanisms. Japanese Society for Chronobiology Magazine 20: 3-7. (Japanese)
Godwin, A.R.* Kojima, S.*, Green, C.B. Wilusz, J. (2013) Kiss your tail goodbye: the role of PARN, Nocturnin, and Angel deadenylases in mRNA biology. Biochim. Biophys. Acta. -Gene Regulatory Mechanisms 1829(6-7):571-579.
Kojima, S. (2013) “The Green lab in the brown land” Japanese Society for Chronobiology Magazine 19(1):38-43. (Japanese)
Kojima, S., Sher-Chen, E.L. Green, C.B. (2012) Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression. Gene. Dev. 26(24):2724-2736.
Niu, S., Shingle, D.L., Garbarino-Pico, E., Kojima, S., Gilbert, M.R., Green, C.B. (2011) The Circadian Deadenylase Nocturnin is Necessary for Stabilization of the iNOS mRNA in Mice. PLoS ONE 6(11):e26954
Kojima, S., Shingle, D.L., Green, C.B. (2011) Post-transcriptional control of circadian rhythms. J.Cell Sci., 124(Pt 3):311-320.
Douris, N*, Kojima, S.*, Pan, X.*, Lerch-Gaggl, A.F., Duong, S.Q., Hussain, M.M., Green, C.B. (2011) Nocturnin Regulates Circadian Trafficking of Dietary Lipid in Intestinal Enterocytes. Curr. Biol. 21:1-9.
Kojima, S., Gatfield, D., Esau, C.C., Green, C.B. (2010) MicroRNA-122 Modulates the Rhythmic Expression Profile of the Circadian Deadenylase Nocturnin in Mouse Liver. PLoS ONE 5(6): e11264.
Kawai,M., Green, C.B., Lecka-Czernik, B., Douris, N., Gilbert, M.R. Kojima, S., Ackert-Bicknell, C., Garg, N., Horowitz, M.C., Adamo,M.L., Clemmons,D.R., Rosen,C.J. (2010) A circadian-regulated gene, Nocturnin, promotes adipogenesis by stimulating PPAR-gamma nuclear translocation. Proc. Natl. Acad. Sci. USA 107 (23) 10508-10513.
Green, C.B*., Douris, N*., Kojima, S., Strayer, C.A., Fogerty, J., Lourim, D., Keller, S.R. and Besharse, J.C. (2007) Loss of Nocturnin, a circadian deadenylase, confers resistance to hepatic steatosis and diet-induced obesity. Proc. Natl. Acad. Sci. USA 104 (23) 9888-9893.
Kojima, S., Matsumoto, K., Hirose, M., Shimada, M., Nagano, M., Shigeyoshi, Y., Hoshino, S., Ui-Tei, K., Saigo, K., Green, C.B. Sakaki, Y., Tei, H. (2007) LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1. Proc. Natl. Acad. Sci. USA, 104 (6), 1859-1864.
Kojima, S., Hirose, M., Tokunaga, K., Sakaki, Y., Tei, H. (2003) Structural and functional analysis of 3' untranslated region of mouse Period1 mRNA. Biochem Biophys Res Commun. 301 (1), 1-7.
Kojima, S., Sakaki, Y., Tei, H. (2002) “The significance of peripheral clocks on feeding behavior” Gendai Iryou. 34, 1367-1391. (Japanese)
Kojima, S., Yanagihara, I., Kono, G., Sugahara, T., Nasu, H., Kijima, M., Hattori, A., Kodama, T., Nagayama, K.I., Honda, T. (2000) mkp-1 encoding mitogen-activated protein kinase phosphatase 1, a verotoxin 1 responsive gene, detected by differential display reverse transcription-PCR in Caco-2 cells. Infect. Immun. 68 (5), 2791-2796.
Kojima, S., Honda, T. (2000) “Infectious Enteritis” Shoukaki no Rinsho. 3, 249-257. (Japanese)
Yanagihara, I., Kojima, S., Honda, T. (1999) “Considering food poisoning. Intestinal hemorrhagic Escherichia coli O 157.” Japan Medical Journal. 3919, 22-29. (Japanese)
* Equally contributed authors
Godwin, A.R.* Kojima, S.*, Green, C.B. Wilusz, J. (2013) Kiss your tail goodbye: the role of PARN, Nocturnin, and Angel deadenylases in mRNA biology. Biochim. Biophys. Acta. -Gene Regulatory Mechanisms 1829(6-7):571-579.
Kojima, S. (2013) “The Green lab in the brown land” Japanese Society for Chronobiology Magazine 19(1):38-43. (Japanese)
Kojima, S., Sher-Chen, E.L. Green, C.B. (2012) Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression. Gene. Dev. 26(24):2724-2736.
Niu, S., Shingle, D.L., Garbarino-Pico, E., Kojima, S., Gilbert, M.R., Green, C.B. (2011) The Circadian Deadenylase Nocturnin is Necessary for Stabilization of the iNOS mRNA in Mice. PLoS ONE 6(11):e26954
Kojima, S., Shingle, D.L., Green, C.B. (2011) Post-transcriptional control of circadian rhythms. J.Cell Sci., 124(Pt 3):311-320.
Douris, N*, Kojima, S.*, Pan, X.*, Lerch-Gaggl, A.F., Duong, S.Q., Hussain, M.M., Green, C.B. (2011) Nocturnin Regulates Circadian Trafficking of Dietary Lipid in Intestinal Enterocytes. Curr. Biol. 21:1-9.
Kojima, S., Gatfield, D., Esau, C.C., Green, C.B. (2010) MicroRNA-122 Modulates the Rhythmic Expression Profile of the Circadian Deadenylase Nocturnin in Mouse Liver. PLoS ONE 5(6): e11264.
Kawai,M., Green, C.B., Lecka-Czernik, B., Douris, N., Gilbert, M.R. Kojima, S., Ackert-Bicknell, C., Garg, N., Horowitz, M.C., Adamo,M.L., Clemmons,D.R., Rosen,C.J. (2010) A circadian-regulated gene, Nocturnin, promotes adipogenesis by stimulating PPAR-gamma nuclear translocation. Proc. Natl. Acad. Sci. USA 107 (23) 10508-10513.
Green, C.B*., Douris, N*., Kojima, S., Strayer, C.A., Fogerty, J., Lourim, D., Keller, S.R. and Besharse, J.C. (2007) Loss of Nocturnin, a circadian deadenylase, confers resistance to hepatic steatosis and diet-induced obesity. Proc. Natl. Acad. Sci. USA 104 (23) 9888-9893.
Kojima, S., Matsumoto, K., Hirose, M., Shimada, M., Nagano, M., Shigeyoshi, Y., Hoshino, S., Ui-Tei, K., Saigo, K., Green, C.B. Sakaki, Y., Tei, H. (2007) LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1. Proc. Natl. Acad. Sci. USA, 104 (6), 1859-1864.
Kojima, S., Hirose, M., Tokunaga, K., Sakaki, Y., Tei, H. (2003) Structural and functional analysis of 3' untranslated region of mouse Period1 mRNA. Biochem Biophys Res Commun. 301 (1), 1-7.
Kojima, S., Sakaki, Y., Tei, H. (2002) “The significance of peripheral clocks on feeding behavior” Gendai Iryou. 34, 1367-1391. (Japanese)
Kojima, S., Yanagihara, I., Kono, G., Sugahara, T., Nasu, H., Kijima, M., Hattori, A., Kodama, T., Nagayama, K.I., Honda, T. (2000) mkp-1 encoding mitogen-activated protein kinase phosphatase 1, a verotoxin 1 responsive gene, detected by differential display reverse transcription-PCR in Caco-2 cells. Infect. Immun. 68 (5), 2791-2796.
Kojima, S., Honda, T. (2000) “Infectious Enteritis” Shoukaki no Rinsho. 3, 249-257. (Japanese)
Yanagihara, I., Kojima, S., Honda, T. (1999) “Considering food poisoning. Intestinal hemorrhagic Escherichia coli O 157.” Japan Medical Journal. 3919, 22-29. (Japanese)
* Equally contributed authors
