Updated on 2021/03/15

写真a

 
OGAMI Koichi
 
Organization
Graduate School of Medicine Center for Neural Disease and Cancer Division Assistant Professor
Graduate School
Graduate School of Medicine
Undergraduate School
School of Medicine Department of Medicine
Title
Assistant Professor

Degree 1

  1. 博士(薬学) ( 2013.3   名古屋市立大学 ) 

Research Interests 3

  1. 相分離

  2. ゲノム

  3. RNA

Research Areas 5

  1. Life Science / Molecular biology

  2. Life Science / System genome science

  3. Life Science / Cell biology

  4. Life Science / Molecular biology

  5. Life Science / Genome biology

Research History 5

  1. Nagoya University   Graduate School of Medicine   Assistant Professor

    2020.12

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    Country:Japan

  2. Nagoya City University   Assistant Professor

    2018.1 - 2020.11

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    Country:Japan

  3. RIKEN   RIKEN Center for Life Science Technologies   Researcher

    2016.11 - 2017.12

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    Country:Japan

  4. Columbia University   Biological Sciences   Researcher

    2013.11 - 2016.10

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    Country:Japan

  5. Nagoya City University   Researcher

    2013.4 - 2013.10

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    Country:Japan

Education 2

  1. Nagoya City University   Graduate School, Division of Pharmaceutical Sciences

    - 2013.3

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    Country: Japan

  2. Nagoya City University   Faculty of Pharmaceutical Science

    - 2008.3

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    Country: Japan

 

Papers 15

  1. Widespread transcript shortening through alternative polyadenylation in secretory cell differentiation Reviewed

    Larry C. Cheng, Dinghai Zheng, Erdene Baljinnyam, Fangzheng Sun, Koichi Ogami, Percy Luk Yeung, Mainul Hoque, Chi-Wei Lu, James L. Manley, Bin Tian

    Nature Communications   Vol. 11 ( 1 )   2020.12

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    Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1038/s41467-020-16959-2

    Scopus

    Other Link: http://www.nature.com/articles/s41467-020-16959-2

  2. ABCE1 Acts as a Positive Regulator of Exogenous RNA Decay. Reviewed International journal

    Takuto Nogimori*, Koichi Ogami*, Yuka Oishi, Ryoya Goda, Nao Hosoda, Yoshiaki Kitamura, Yukio Kitade, Shin-Ichi Hoshino

    Viruses   Vol. 12 ( 2 )   2020.2

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    The 2'-5'-oligoadenylate synthetase (OAS)/RNase L system protects hosts against pathogenic viruses through cleavage of the exogenous single-stranded RNA. In this system, an evolutionally conserved RNA quality control factor Dom34 (known as Pelota (Pelo) in higher eukaryotes) forms a surveillance complex with RNase L to recognize and eliminate the exogenous RNA in a manner dependent on translation. Here, we newly identified that ATP-binding cassette sub-family E member 1 (ABCE1), which is also known as RNase L inhibitor (RLI), is involved in the regulation of exogenous RNA decay. ABCE1 directly binds to form a complex with RNase L and accelerates RNase L dimer formation in the absence of 2'-5' oligoadenylates (2-5A). Depletion of ABCE1 represses 2-5A-induced RNase L activation and stabilizes exogenous RNA to a level comparable to that seen in RNase L depletion. The increased half-life of the RNA by the single depletion of either protein is not significantly affected by the double depletion of both proteins, suggesting that RNase L and ABCE1 act together to eliminate exogenous RNA. Our results indicate that ABCE1 functions as a positive regulator of exogenous RNA decay rather than an inhibitor of RNase L.

    DOI: 10.3390/v12020174

    Scopus

  3. The RNA-binding protein QKI-7 recruits the poly(A) polymerase GLD-2 for 3' adenylation and selective stabilization of microRNA-122. Reviewed International journal

    Hiroaki Hojo, Yuka Yashiro, Yuta Noda, Koichi Ogami, Ryota Yamagishi, Shunpei Okada, Shin-Ichi Hoshino, Tsutomu Suzuki

    The Journal of biological chemistry   Vol. 295 ( 2 ) page: 390 - 402   2020.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    MicroRNA-122 (miR-122) is highly expressed in hepatocytes, where it plays an important role in regulating cholesterol and fatty acid metabolism, and it is also a host factor required for hepatitis C virus replication. miR-122 is selectively stabilized by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2 (also known as PAPD4 or TENT2). However, it is unclear how GLD-2 specifically stabilizes miR-122. Here, we show that QKI7 KH domain-containing RNA binding (QKI-7), one of three isoforms of the QKI proteins, which are members of the signal transduction and activation of RNA (STAR) family of RNA-binding proteins, is involved in miR-122 stabilization. QKI down-regulation specifically decreased the steady-state level of mature miR-122, but did not affect the pre-miR-122 level. We also found that QKI-7 uses its C-terminal region to interact with GLD-2 and its QUA2 domain to associate with the RNA-induced silencing complex protein Argonaute 2 (Ago2), indicating that the GLD-2-QKI-7 interaction recruits GLD-2 to Ago2. QKI-7 exhibited specific affinity to miR-122 and significantly promoted GLD-2-mediated 3' adenylation of miR-122 in vitro Taken together, our findings indicate that miR-122 binds Ago2-interacting QKI-7, which recruits GLD-2 for 3' adenylation and stabilization of miR-122.

    DOI: 10.1074/jbc.RA119.011617

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  4. Efficient differentiation and purification of human induced pluripotent stem cell-derived endothelial progenitor cells and expansion with the use of inhibitors of ROCK, TGF-β, and GSK3β Reviewed

    Hiromasa Aoki, Misaki Yamashita, Tadahiro Hashita, Koichi Ogami, Shinichi Hoshino, Takahiro Iwao, Tamihide Matsunaga

    Heliyon   Vol. 6 ( 3 ) page: e03493 - e03493   2020.3

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.heliyon.2020.e03493

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  5. A novel method for stabilizing microRNA mimics Reviewed International journal

    Takuto Nogimori, Kazuya Furutachi, Koichi Ogami, Nao Hosoda, Shin-ichi Hoshino

    Biochemical and Biophysical Research Communications   Vol. 511 ( 2 ) page: 422 - 426   2019.4

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.bbrc.2019.02.075

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  6. Large expert-curated database for benchmarking document similarity detection in biomedical literature search Reviewed International journal

    Brown P., RELISH consortium, Zhou Y.

    Database   Vol. 2019   page: 1 - 67   2019.10

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/database/baz085

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  7. NRDE-2, the human homolog of fission yeast Nrl1, prevents DNA damage accumulation in human cells Reviewed International journal

    Richard P*, Ogami K*, Chen Y, Feng S, Moresco JJ, Yates JR, Manley JL

    RNA Biology   Vol. 15 ( 7 ) page: 868 - 876   2018.6

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    Authorship:Lead author   Publishing type:Research paper (scientific journal)  

    DOI: 10.1080/15476286.2018.1467180

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  8. RNA surveillance by the nuclear RNA exosome: Mechanisms and significance Reviewed International journal

    Koichi Ogami, Yaqiong Chen, James L. Manley

    Non-coding RNA   Vol. 4 ( 1 ) page: 8   2018.3

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:MDPI AG  

    The nuclear RNA exosome is an essential and versatile machinery that regulates maturation and degradation of a huge plethora of RNA species. The past two decades have witnessed remarkable progress in understanding the whole picture of its RNA substrates and the structural basis of its functions. In addition to the exosome itself, recent studies focusing on associated co-factors have been elucidating how the exosome is directed towards specific substrates. Moreover, it has been gradually realized that loss-of-function of exosome subunits affect multiple biological processes, such as the DNA damage response, R-loop resolution, maintenance of genome integrity, RNA export, translation, and cell differentiation. In this review, we summarize the current knowledge of the mechanisms of nuclear exosome-mediated RNA metabolism and discuss their physiological significance.

    DOI: 10.3390/ncrna4010008

    Scopus

  9. MicroRNP-mediated translational activation of nonadenylated mRNAs in a mammalian cell-free system Reviewed International journal

    Motoaki Wakiyama, Koichi Ogami, Ryo Iwaoka, Kazuma Aoki, Shin-Ichi Hoshino

    Genes to Cells   Vol. 23 ( 5 ) page: 332 - 344   2018.5

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Blackwell Publishing Ltd  

    MicroRNAs are small noncoding RNAs that regulate translation and mRNA stability by binding target mRNAs in complex with Argonaute (AGO) proteins. AGO interacts with a member of the TNRC6 family proteins to form a microRNP complex, which recruits the CCR4-NOT complex to accelerate deadenylation and inhibits translation. MicroRNAs primarily repress translation of target mRNAs but have been shown to enhance translation of a specific type of target reporter mRNAs in various experimental systems: G0 quiescent mammalian cells, Xenopus laevis oocytes, Drosophila embryo extracts, and HeLa cells. In all of the cases mentioned, a common feature of the activated target mRNAs is the lack of a poly(A) tail. Here, we show let-7-microRNP-mediated translational activation of nonadenylated target mRNAs in a mammalian cell-free system, which contains over-expressed AGO2, TNRC6B, and PAPD7 (TUTase5, TRF4-1). Importantly, translation of nonadenylated mRNAs was activated also by tethered TNRC6B silencing domain (SD), in the presence of PAPD7. Deletion of the poly(A)-binding protein (PABP) interacting motif (PAM2) from the TNRC6B-SD abolished the translational activation, suggesting the involvement of PABP in the process. Similar results were also obtained in cultured HEK293T cells. This work may provide novel insights into microRNP-mediated mRNA regulation.

    DOI: 10.1111/gtc.12580

    Scopus

  10. An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression Reviewed

    Koichi Ogami, Patricia Richard, Yaqiong Chen, Mainul Hoque, Wencheng Li, James J. Moresco, John R. Yates, Bin Tian, James L. Manley

    GENES & DEVELOPMENT   Vol. 31 ( 12 ) page: 1257 - 1271   2017.6

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT  

    Many long noncoding RNAs (lncRNAs) are unstable and rapidly degraded in the nucleus by the nuclear exosome. An exosome adaptor complex called NEXT (nuclear exosome targeting) functions to facilitate turnover of some of these lncRNAs. Here we show that knockdown of one NEXT subunit, Mtr4, but neither of the other two subunits, resulted in accumulation of two types of lncRNAs: prematurely terminated RNAs (ptRNAs) and upstream antisense RNAs (uaRNAs). This suggested a NEXT-independent Mtr4 function, and, consistent with this, we isolated a distinct complex containing Mtr4 and the zinc finger protein ZFC3H1. Strikingly, knockdown of either protein not only increased pt/uaRNA levels but also led to their accumulation in the cytoplasm. Furthermore, all pt/uaRNAs examined associated with active ribosomes, but, paradoxically, this correlated with a global reduction in heavy polysomes and overall repression of translation. Our findings highlight a critical role for Mtr4/ZFC3H1 in nuclear surveillance of naturally unstable lncRNAs to prevent their accumulation, transport to the cytoplasm, and resultant disruption of protein synthesis.

    DOI: 10.1101/gad.302604.117

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  11. Mtr4/ZFC3H1 protects polysomes through nuclear RNA surveillance Reviewed

    Koichi Ogami, James L. Manley

    Cell Cycle   Vol. 16 ( 21 ) page: 1999 - 2000   2017.11

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Taylor and Francis Inc.  

    DOI: 10.1080/15384101.2017.1377501

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  12. Antiproliferative protein Tob directly regulates c-myc proto-oncogene expression through cytoplasmic polyadenylation element-binding protein CPEB Reviewed

    K. Ogami, N. Hosoda, Y. Funakoshi, S. Hoshino

    ONCOGENE   Vol. 33 ( 1 ) page: 55 - 64   2014.1

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

    The regulation of mRNA deadenylation constitutes a pivotal mechanism of the post-transcriptional control of gene expression. Here we show that the antiproliferative protein Tob, a component of the Caf1-Ccr4 deadenylase complex, is involved in regulating the expression of the proto-oncogene c-myc. The c-myc mRNA contains cis elements (CPEs) in its 3'-untranslated region (3'-UTR), which are recognized by the cytoplasmic polyadenylation element-binding protein (CPEB). CPEB recruits Caf1 deadenylase through interaction with Tob to form a ternary complex, CPEB-Tob-Caf1, and negatively regulates the expression of c-myc by accelerating the deadenylation and decay of its mRNA. In quiescent cells, c-myc mRNA is destabilized by the trans-acting complex (CPEB-Tob-Caf1), while in cells stimulated by the serum, both Tob and Caf1 are released from CPEB, and c-Myc expression is induced early after stimulation by the stabilization of its mRNA as an 'immediate-early gene'. Collectively, these results indicate that Tob is a key factor in the regulation of c-myc gene expression, which is essential for cell growth. Thus, Tob appears to function in the control of cell growth at least, in part, by regulating the expression of c-myc.

    DOI: 10.1038/onc.2012.548

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  13. RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3 ' UTRs Reviewed

    Dafne Campigli Di Giammartino, Wencheng Li, Koichi Ogami, Jossie J. Yashinskie, Mainul Hoque, Bin Tian, James L. Manley

    GENES & DEVELOPMENT   Vol. 28 ( 20 ) page: 2248 - 2260   2014.10

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT  

    Polyadenylation of mRNA precursors is mediated by a large multisubunit protein complex. Here we show that RBBP6 (retinoblastoma-binding protein 6), identified initially as an Rb- and p53-binding protein, is a component of this complex and functions in 3' processing in vitro and in vivo. RBBP6 associates with other core factors, and this interaction is mediated by an unusual ubiquitin-like domain, DWNN ("domain with no name"), that is required for 3' processing activity. The DWNN is also expressed, via alternative RNA processing, as a small single-domain protein (isoform 3 [iso3]). Importantly, we show that iso3, known to be down-regulated in several cancers, competes with RBBP6 for binding to the core machinery, thereby inhibiting 3' processing. Genome-wide analyses following RBBP6 knockdown revealed decreased transcript levels, especially of mRNAs with AU-rich 3' untranslated regions (UTRs) such as c-Fos and c-Jun, and increased usage of distal poly(A) sites. Our results implicate RBBP6 and iso3 as novel regulators of 3' processing, especially of RNAs with AU-rich 3' UTRs.

    DOI: 10.1101/gad.245787.114

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  14. Molecular cloning and characterization of a novel isoform of the non-canonical poly(A) polymerase PAPD7 Reviewed

    Koichi Ogami, Rihe Cho, Shin-ichi Hoshino

    Biochemical and Biophysical Research Communications   Vol. 432 ( 1 ) page: 135 - 140   2013.3

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    Non-canonical poly(A) polymerases (ncPAPs) catalyze the addition of poly(A) tail to the 3' end of RNA to play pivotal roles in the regulation of gene expression and also in quality control. Here we identified a novel isoform of the 7th member of ncPAPs: PAPD7 (PAPD7 l), which contains 230 extra amino acids at the amino terminus of the previously identified PAPD7 (PAPD7 s). In sharp contrast to the inactive PAPD7 s, PAPD7 l showed robust nucleotidyl transferase activity when tethered to an RNA. A region required for the activity was localized to 187-219 aa, and this region was also required for the nuclear retention of PAPD7 l. Western blot analysis revealed that 94. kDa band (corresponding to PAPD7 l) but not 62. kDa band (corresponding to PAPD7 s) detected by PAPD7 antibody was specifically depleted by treatment with PAPD7 siRNA in both HeLa and U2OS cells. These results suggest that PAPD7 l is the major and active isoform of PAPD7 expressed in cells. © 2013 Elsevier Inc.

    DOI: 10.1016/j.bbrc.2013.01.072

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    Other Link: http://orcid.org/0000-0001-9380-9666

  15. Anti-proliferative protein Tob negatively regulates CPEB3 target by recruiting Caf1 deadenylase Reviewed

    Nao Hosoda, Yuji Funakoshi, Masato Hirasawa, Ryota Yamagishi, Yukako Asano, Ryu Miyagawa, Koichi Ogami, Masafumi Tsujimoto, Shin-ichi Hoshino

    EMBO JOURNAL   Vol. 30 ( 7 ) page: 1311 - 1323   2011.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

    Tob is a member of the anti-proliferative protein family, which functions in transcription and mRNA decay. We have previously demonstrated that Tob is involved in the general mechanism of mRNA decay by mediating mRNA deadenylation through interaction with Caf1 and a general RNA-binding protein, PABPC1. Here, we focus on the role of Tob in the regulation of specific mRNA. We show that Tob binds directly to a sequence-specific RNA-binding protein, cytoplasmic polyadenylation element-binding protein 3 (CPEB3). CPEB3 negatively regulates the expression of a target by accelerating deadenylation and decay of its mRNA, which it achieves by tethering to the mRNA. The carboxyl-terminal RNA-binding domain of CPEB3 binds to the carboxyl-terminal unstructured region of Tob. Tob then binds Caf1 deadenylase and recruits it to CPEB3 to form a ternary complex. The CPEB3-accelerated deadenylation was abrogated by a dominant-negative mutant of either Caf1 or Tob. Together, these results indicate that Tob mediates the recruitment of Caf1 to the target of CPEB3 and elicits deadenylation and decay of the mRNA. Our results provide an explanation of how Tob regulates specific biological processes. The EMBO Journal (2011) 30, 1311-1323. doi: 10.1038/emboj.2011.37; Published online 18 February 2011

    DOI: 10.1038/emboj.2011.37

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    Other Link: http://orcid.org/0000-0001-9380-9666

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MISC 2

  1. がん抑制遺伝子産物TobによるmRNA分解を介したがん抑制と学習記憶の調節

    Ogami K, Hoshino SI

    ファルマシア   Vol. 51 ( 1 ) page: 27 - 31   2015.1

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    Language:English  

  2. Research on mRNA degradation and drug discovery Reviewed

    Ogami K, Hoshino S

    Folia Pharmacologica Japonica   Vol. 136 ( 3 ) page: 150-154   2010

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Presentations 4

  1. Poly(A) tail length positively correlates with the extent of mRNA ribosome loading

    Koichi Ogami, Yuka Oishi, Natsumi Yamaguchi, Shin-ichi Hoshino

    Cold Spring Harbor Laboratory meeting: Translational Control (Virtual)  2020.9 

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    Event date: 2020.9

    Language:English   Presentation type:Oral presentation (general)  

  2. Nulcear surveillance of polyadenylated lncRNAs by Mtr4/ZFC3H1 Invited International conference

    Ogami K

    The 24th Tokyo RNA Club  2017.12.11 

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    Event date: 2017.12

    Language:English   Presentation type:Oral presentation (invited, special)  

  3. An Mtr4/ ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression International conference

    Ogami K, Chen Y, Richard P, Hoque M, Li W, Moresco JJ, Yates JR, Tian B, Manley JL

    Cold Spring Harbor Laboratory meeting: Eukaryotic mRNA Processing  2017.8 

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    Event date: 2017.8

    Language:English   Presentation type:Oral presentation (general)  

  4. The RNA helicase Mtr4 regulates accumulation of multiple types of lncRNA in human cells. International conference

    Ogami K, Hoque M, Li W, Tian B, Manley JL

    Cold Spring Harbor Laboratory meeting: Eukaryotic mRNA Processing  2015.8 

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    Event date: 2015.8

    Language:English   Presentation type:Oral presentation (general)  

KAKENHI (Grants-in-Aid for Scientific Research) 2

  1. Correlation between mRNA poly(A) tail length and translational activity

    Grant number:20K15719  2020.4 - 2022.3

    Grant-in-Aid for Early-Career Scientists

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    Authorship:Principal investigator 

    Grant amount:\4290000 ( Direct Cost: \3300000 、 Indirect Cost:\990000 )

  2. CPEB-mediated post-transcriptional regulation of gene expression

    Grant number:18K14630  2018.4 - 2020.3

    Grant-in-Aid for Early-Career Scientists

    Ogami Koichi

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    Authorship:Principal investigator 

    Grant amount:\4160000 ( Direct Cost: \3200000 、 Indirect Cost:\960000 )

    The RNA-binding protein CPEB regulates gene expression both positively and negatively. Currently, c-myc mRNA is the only known target that is promptly degraded by a mechanism involving CPEB. In this study, we identified an RNA code comprising of the consesnsus and non-consesnsus CPE sequences that guides CPEB to degrade c-myc mRNA. We also worked on CPEB's role during DNA damage responses, and found that CPEB and its binding poly(A) polymerase PAPD7 are essential for the increase of RNR2 protein after doxorubicin or UV treatment of U2OS cells. While many of the constitutively expressed mRNAs are deadenylated in response to the DNA damages, poly(A) tails of RNR2 mRNA are elongated. Our results suggesting that CPEB-PAPD7 discriminates RNR2 mRNA from the others to indeuce translation during DNA damage response.