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4. Delayed Degradation and Impaired Dendritic Delivery of Intron-Lacking EGFP-Arc/Arg3.1 mRNA in EGFP-Arc Transgenic Mice

Author

Steward, Oswald, Yee, Kelly Matsudaira, Farris, Shannon, Pirbhoy, Patricia S, Worley, Paul, Okamura, Kohji, Okuno, Hiroyuki, and Bito, Haruhiko

Subjects
Genetics, 1.1 Normal biological development and functioning, Underpinning research, Neurological, LTP, synaptic plasticity, protein synthesis, dendrite, dendritic mRNA, dendritic spines, immediate early gene, nonsense-mediated decay, Clinical Sciences, Neurosciences
Abstract

Arc is a unique immediate early gene (IEG) whose expression is induced as synapses are modified during learning. Newly-synthesized Arc mRNA is rapidly transported throughout dendrites and localizes near recently activated synapses. Arc mRNA levels are regulated by rapid degradation, which is accelerated by synaptic activity in a translation-dependent process. One possible mechanism is nonsense-mediated mRNA decay (NMD), which depends on the presence of a splice junction in the 3'UTR. Here, we test this hypothesis using transgenic mice that express EGFP-Arc. Because the transgene was constructed from Arc cDNA, it lacks intron structures in the 3'UTR that are present in the endogenous Arc gene. NMD depends on the presence of proteins of the exon junction complex (EJC) downstream of a stop codon, so EGFP-Arc mRNA should not undergo NMD. Assessment of Arc mRNA rundown in the presence of the transcription inhibitor actinomycin-D confirmed delayed degradation of EGFP-Arc mRNA. EGFP-Arc mRNA and protein are expressed at much higher levels in transgenic mice under basal and activated conditions but EGFP-Arc mRNA does not enter dendrites efficiently. In a physiological assay in which cycloheximide (CHX) was infused after induction of Arc by seizures, there were increases in endogenous Arc mRNA levels consistent with translation-dependent Arc mRNA decay but this was not seen with EGFP-Arc mRNA. Taken together, our results indicate: (1) Arc mRNA degradation occurs via a mechanism with characteristics of NMD; (2) rapid dendritic delivery of newly synthesized Arc mRNA after induction may depend in part on prior splicing of the 3'UTR.

Published
2018

5. NUDT15 variants confer high incidence of second malignancies in children with acute lymphoblastic leukemia

Author

Yoshida, Masanori, Nakabayashi, Kazuhiko, Yang, Wentao, Sato-Otsubo, Aiko, Tsujimoto, Shin-ichi, Ogata-Kawata, Hiroko, Kawai, Tomoko, Ishiwata, Keisuke, Sakamoto, Mika, Okamura, Kohji, Yoshida, Kaoru, Shirai, Ryota, Osumi, Tomoo, Moriyama, Takaya, Nishii, Rina, Takahashi, Hiroyuki, Kiyotani, Chikako, Shioda, Yoko, Terashima, Keita, Ishimaru, Sae, Yuza, Yuki, Takagi, Masatoshi, Arakawa, Yuki, Kinoshita, Akitoshi, Hino, Moeko, Imamura, Toshihiko, Hasegawa, Daisuke, Nakazawa, Yozo, Okuya, Mayuko, Kakuda, Harumi, Takasugi, Nao, Inoue, Akiko, Ohki, Kentaro, Yoshioka, Takako, Ito, Shuichi, Tomizawa, Daisuke, Koh, Katsuyoshi, Matsumoto, Kimikazu, Sanada, Masashi, Kiyokawa, Nobutaka, Ohara, Akira, Ogawa, Seishi, Manabe, Atsushi, Niwa, Akira, Hata, Kenichiro, Yang, Jun J., and Kato, Motohiro

Published
2021
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7. Delayed Degradation and Impaired Dendritic Delivery of Intron-Lacking EGFP-Arc/Arg3.1 mRNA in EGFP-Arc Transgenic Mice.

Author

Steward, Oswald, Matsudaira Yee, Kelly, Farris, Shannon, Pirbhoy, Patricia S, Worley, Paul, Okamura, Kohji, Okuno, Hiroyuki, and Bito, Haruhiko

Subjects
LTP, dendrite, dendritic mRNA, dendritic spines, immediate early gene, nonsense-mediated decay, protein synthesis, synaptic plasticity, Genetics, 1.1 Normal biological development and functioning, Neurological, Neurosciences, Clinical Sciences
Abstract

Arc is a unique immediate early gene (IEG) whose expression is induced as synapses are modified during learning. Newly-synthesized Arc mRNA is rapidly transported throughout dendrites and localizes near recently activated synapses. Arc mRNA levels are regulated by rapid degradation, which is accelerated by synaptic activity in a translation-dependent process. One possible mechanism is nonsense-mediated mRNA decay (NMD), which depends on the presence of a splice junction in the 3'UTR. Here, we test this hypothesis using transgenic mice that express EGFP-Arc. Because the transgene was constructed from Arc cDNA, it lacks intron structures in the 3'UTR that are present in the endogenous Arc gene. NMD depends on the presence of proteins of the exon junction complex (EJC) downstream of a stop codon, so EGFP-Arc mRNA should not undergo NMD. Assessment of Arc mRNA rundown in the presence of the transcription inhibitor actinomycin-D confirmed delayed degradation of EGFP-Arc mRNA. EGFP-Arc mRNA and protein are expressed at much higher levels in transgenic mice under basal and activated conditions but EGFP-Arc mRNA does not enter dendrites efficiently. In a physiological assay in which cycloheximide (CHX) was infused after induction of Arc by seizures, there were increases in endogenous Arc mRNA levels consistent with translation-dependent Arc mRNA decay but this was not seen with EGFP-Arc mRNA. Taken together, our results indicate: (1) Arc mRNA degradation occurs via a mechanism with characteristics of NMD; (2) rapid dendritic delivery of newly synthesized Arc mRNA after induction may depend in part on prior splicing of the 3'UTR.

Published
2017

10. Prevalence of pathogenic variants in cancer‐predisposing genes in second cancer after childhood solid cancers

Author

Yoshida, Masanori, primary, Nakabayashi, Kazuhiko, additional, Yang, Wentao, additional, Sato‐Otsubo, Aiko, additional, Tsujimoto, Shin‐ichi, additional, Ogata‐Kawata, Hiroko, additional, Kawai, Tomoko, additional, Ishiwata, Keisuke, additional, Sakamoto, Mika, additional, Okamura, Kohji, additional, Yoshida, Kaoru, additional, Shirai, Ryota, additional, Osumi, Tomoo, additional, Kiyotani, Chikako, additional, Shioda, Yoko, additional, Terashima, Keita, additional, Ishimaru, Sae, additional, Yuza, Yuki, additional, Takagi, Masatoshi, additional, Arakawa, Yuki, additional, Imamura, Toshihiko, additional, Hasegawa, Daisuke, additional, Inoue, Akiko, additional, Yoshioka, Takako, additional, Ito, Shuichi, additional, Tomizawa, Daisuke, additional, Koh, Katsuyoshi, additional, Matsumoto, Kimikazu, additional, Kiyokawa, Nobutaka, additional, Ogawa, Seishi, additional, Manabe, Atsushi, additional, Niwa, Akira, additional, Hata, Kenichiro, additional, Yang, Jun J., additional, and Kato, Motohiro, additional

Published
2023
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13. Integrator complex subunit 15 controls mRNA splicing and is critical for eye development

Author

Azuma, Noriyuki, primary, Yokoi, Tadashi, additional, Tanaka, Taku, additional, Matsuzaka, Emiko, additional, Saida, Yuki, additional, Nishina, Sachiko, additional, Terao, Miho, additional, Takada, Shuji, additional, Fukami, Maki, additional, Okamura, Kohji, additional, Maehara, Kayoko, additional, Yamasaki, Tokiwa, additional, Hirayama, Jun, additional, Nishina, Hiroshi, additional, Handa, Hiroshi, additional, and Yamaguchi, Yuki, additional

Published
2023
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17. Nonconditioned ADA-SCID gene therapy reveals ADA requirement in the hematopoietic system and clonal dominance of vector-marked clones

Author

Uchiyama, Toru, primary, Takahashi, Sirirat, additional, Nakabayashi, Kazuhiko, additional, Okamura, Kohji, additional, Edasawa, Kaori, additional, Yamada, Masafumi, additional, Watanabe, Nobuyuki, additional, Mochizuki, Emi, additional, Yasuda, Toru, additional, Miura, Akane, additional, Kato, Motohiro, additional, Tomizawa, Daisuke, additional, Otsu, Makoto, additional, Ariga, Tadashi, additional, and Onodera, Masafumi, additional

Published
2021
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20. Profiling ascidian promoters as the primordial type of vertebrate promoter

Author

Okamura Kohji, Yamashita Riu, Takimoto Noriko, Nishitsuji Koki, Suzuki Yutaka, Kusakabe Takehiro G, and Nakai Kenta

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background CpG islands are observed in mammals and other vertebrates, generally escape DNA methylation, and tend to occur in the promoters of widely expressed genes. Another class of promoter has lower G+C and CpG contents, and is thought to be involved in the spatiotemporal regulation of gene expression. Non-vertebrate deuterostomes are reported to have a single class of promoter with high-frequency CpG dinucleotides, suggesting that this is the original type of promoter. However, the limited annotation of these genes has impeded the large-scale analysis of their promoters. Results To determine the origins of the two classes of vertebrate promoters, we chose Ciona intestinalis, an invertebrate that is evolutionarily close to the vertebrates, and identified its transcription start sites genome-wide using a next-generation sequencer. We indeed observed a high CpG content around the transcription start sites, but their levels in the promoters and background sequences differed much less than in mammals. The CpG-rich stretches were also fairly restricted, so they appeared more similar to mammalian CpG-poor promoters. Conclusions From these data, we infer that CpG islands are not sufficiently ancient to be found in invertebrates. They probably appeared early in vertebrate evolution via some active mechanism and have since been maintained as part of vertebrate promoters.

Published
2011
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21. Global variation in copy number in the human genome

Author

Redon, Richard, Ishikawa, Shumpei, Fitch, Karen R., Feuk, Lars, Perry, George H., Andrews, T. Daniel, Fiegler, Heike, Shapero, Michael H., Carson, Andrew R., Chen, Wenwei, Cho, Eun Kyung, Dallaire, Stephanie, Freeman, Jennifer L., Gonzalez, Juan R., Gratacos, Monica, Huang, Jing, Kalaitzopoulos, Dimitrios, Komura, Daisuke, MacDonald, Jeffrey R., Marshall, Christian R., Mei, Rui, Montgomery, Lyndal, Nishimura, Kunihiro, Okamura, Kohji, Shen, Fan, Somerville, Martin J., Tchinda, Joelle, Valsesia, Armand, Woodwark, Cara, Yang, Fengtang, Zhang, Junjun, Zerjal, Tatiana, Zhang, Jane, Armengol, Lluis, Conrad, Donald F., Estivill, Xavier, Tyler-Smith, Chris, Carter, Nigel P., Aburatani, Hiroyuki, Lee, Charles, Jones, Keith W., Scherer, Stephen W., and Hurles, Matthew E.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Richard Redon [1]; Shumpei Ishikawa [2, 3]; Karen R. Fitch [4]; Lars Feuk [5, 6]; George H. Perry [7]; T. Daniel Andrews [1]; Heike Fiegler [1]; Michael H. Shapero [...]

Published
2006
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22. Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution

Author

Matsumoto Kazuaki A, Okamura Kohji, and Nakai Kenta

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background DNA methylation by the Dnmt family occurs in vertebrates and invertebrates, including ascidians, and is thought to play important roles in gene regulation and genome stability, especially in vertebrates. However, the global methylation patterns of vertebrates and invertebrates are distinctive. Whereas almost all CpG sites are methylated in vertebrates, with the exception of those in CpG islands, the ascidian genome contains approximately equal amounts of methylated and unmethylated regions. Curiously, methylation status can be reliably estimated from the local frequency of CpG dinucleotides in the ascidian genome. Methylated and unmethylated regions tend to have few and many CpG sites, respectively, consistent with our knowledge of the methylation status of CpG islands and other regions in mammals. However, DNA methylation patterns and levels in vertebrates and invertebrates have not been analyzed in the same way. Results Using a new computational methodology based on the decomposition of the bimodal distributions of methylated and unmethylated regions, we estimated the extent of the global methylation patterns in a wide range of animals. We then examined the epigenetic changes in silico along the phylogenetic tree. We observed a gradual transition from fractional to global patterns of methylation in deuterostomes, rather than a clear demarcation between vertebrates and invertebrates. When we applied this methodology to six piscine genomes, some of which showed features similar to those of invertebrates. Conclusions The mammalian global DNA methylation pattern was probably not acquired at an early stage of vertebrate evolution, but gradually expanded from that of a more ancient organism.

Published
2010
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26. Additional file 2: of Transient multifocal genomic crisis creating chromothriptic and non-chromothriptic rearrangements in prezygotic testicular germ cells

Author

Hattori, Atsushi, Okamura, Kohji, Terada, Yumiko, Tanaka, Rika, Katoh-Fukui, Yuko, Matsubara, Yoichi, Matsubara, Keiko, Kagami, Masayo, Horikawa, Reiko, and Fukami, Maki

Abstract

Figure S1. G-banding of the patient. Figure S2. Representative results of the PCR-amplification of DNA fragments containing the fusion junctions. Figure S3. Breakpoint structures of the rearrangements. (PDF 140 kb)

Published
2019
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27. NUDT15variants confer high incidence of second malignancies in children with acute lymphoblastic leukemia

Author

Yoshida, Masanori, Nakabayashi, Kazuhiko, Yang, Wentao, Sato-Otsubo, Aiko, Tsujimoto, Shin-ichi, Ogata-Kawata, Hiroko, Kawai, Tomoko, Ishiwata, Keisuke, Sakamoto, Mika, Okamura, Kohji, Yoshida, Kaoru, Shirai, Ryota, Osumi, Tomoo, Moriyama, Takaya, Nishii, Rina, Takahashi, Hiroyuki, Kiyotani, Chikako, Shioda, Yoko, Terashima, Keita, Ishimaru, Sae, Yuza, Yuki, Takagi, Masatoshi, Arakawa, Yuki, Kinoshita, Akitoshi, Hino, Moeko, Imamura, Toshihiko, Hasegawa, Daisuke, Nakazawa, Yozo, Okuya, Mayuko, Kakuda, Harumi, Takasugi, Nao, Inoue, Akiko, Ohki, Kentaro, Yoshioka, Takako, Ito, Shuichi, Tomizawa, Daisuke, Koh, Katsuyoshi, Matsumoto, Kimikazu, Sanada, Masashi, Kiyokawa, Nobutaka, Ohara, Akira, Ogawa, Seishi, Manabe, Atsushi, Niwa, Akira, Hata, Kenichiro, Yang, Jun J., and Kato, Motohiro

Abstract

The effect of genetic variation on second malignant neoplasms (SMNs) remains unclear. First, we identified the pathogenic germline variants in cancer-predisposing genes among 15 children with SMNs after childhood leukemia/lymphoma using whole-exome sequencing. Because the prevalence was low, we focused on the association between SMNs and NUDT15in primary acute lymphoblastic leukemia (ALL) cases. NUDT15is one of the 6-mercaptopurine (6-MP) metabolic genes, and its variants are common in East Asian individuals. The prevalence of NUDT15hypomorphic variants was higher in patients with SMNs (n = 14; 42.9%) than in the general population in the gnomAD database (19.7%; P= .042). In the validation study with a cohort of 438 unselected patients with ALL, the cumulative incidence of SMNs was significantly higher among those with (3.0%; 95% confidence interval [CI], 0.6% to 9.4%) than among those without NUDT15variants (0.3%; 95% CI, 0.0% to 1.5%; P= .045). The 6-MP dose administered to patients with ALL with a NUDT15variant was higher than that given to those without SMNs (P= .045). The 6-MP–related mutational signature was observed in SMN specimens after 6-MP exposure. In cells exposed to 6-MP, a higher level of 6-MP induced DNA damage in NUDT15-knockdown induced pluripotent stem cells. Our study indicates that NUDT15variants may confer a risk of SMNs after treatment with 6-MP in patients with ALL.

Published
2021
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28. Evolutionary implications of inversions that have caused intra-strand parity in DNA

Author

Wei John, Okamura Kohji, and Scherer Stephen W

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Chargaff's rule of DNA base composition, stating that DNA comprises equal amounts of adenine and thymine (%A = %T) and of guanine and cytosine (%C = %G), is well known because it was fundamental to the conception of the Watson-Crick model of DNA structure. His second parity rule stating that the base proportions of double-stranded DNA are also reflected in single-stranded DNA (%A = %T, %C = %G) is more obscure, likely because its biological basis and significance are still unresolved. Within each strand, the symmetry of single nucleotide composition extends even further, being demonstrated in the balance of di-, tri-, and multi-nucleotides with their respective complementary oligonucleotides. Results Here, we propose that inversions are sufficient to account for the symmetry within each single-stranded DNA. Human mitochondrial DNA does not demonstrate such intra-strand parity, and we consider how its different functional drivers may relate to our theory. This concept is supported by the recent observation that inversions occur frequently. Conclusion Along with chromosomal duplications, inversions must have been shaping the architecture of genomes since the origin of life.

Published
2007
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30. Recurrent RARB Translocations in Acute Promyelocytic Leukemia Lacking RARA Translocation

Author

Osumi, Tomoo, primary, Tsujimoto, Shin-ichi, additional, Tamura, Moe, additional, Uchiyama, Meri, additional, Nakabayashi, Kazuhiko, additional, Okamura, Kohji, additional, Yoshida, Masanori, additional, Tomizawa, Daisuke, additional, Watanabe, Akihiro, additional, Takahashi, Hiroyuki, additional, Hori, Tsukasa, additional, Yamamoto, Shohei, additional, Hamamoto, Kazuko, additional, Migita, Masahiro, additional, Ogata-Kawata, Hiroko, additional, Uchiyama, Toru, additional, Kizawa, Hiroe, additional, Ueno-Yokohata, Hitomi, additional, Shirai, Ryota, additional, Seki, Masafumi, additional, Ohki, Kentaro, additional, Takita, Junko, additional, Inukai, Takeshi, additional, Ogawa, Seishi, additional, Kitamura, Toshio, additional, Matsumoto, Kimikazu, additional, Hata, Kenichiro, additional, Kiyokawa, Nobutaka, additional, Goyama, Susumu, additional, and Kato, Motohiro, additional

Published
2018
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33. Molecular characteristics of the KCNJ5 mutated aldosterone-producing adenomas

Author

Murakami, Masanori, primary, Yoshimoto, Takanobu, additional, Nakabayashi, Kazuhiko, additional, Nakano, Yujiro, additional, Fukaishi, Takahiro, additional, Tsuchiya, Kyoichiro, additional, Minami, Isao, additional, Bouchi, Ryotaro, additional, Okamura, Kohji, additional, Fujii, Yasuhisa, additional, Hashimoto, Koshi, additional, Hata, Ken-ichiro, additional, Kihara, Kazunori, additional, and Ogawa, Yoshihiro, additional

Published
2017
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34. A novel missense variant of the GNAI3gene and recognisable morphological characteristics of the mandibula in ARCND1

Author

Yanagi, Kumiko, Morimoto, Noriko, Iso, Manami, Abe, Yukimi, Okamura, Kohji, Nakamura, Tomoo, Matsubara, Yoichi, and Kaname, Tadashi

Abstract

Auriculocondylar syndrome (ARCND) is an autosomal monogenic disorder characterised by external ear abnormalities and micrognathia due to hypoplasia of the mandibular rami, condyle and coronoid process. Genetically, three subtypes of ARCND (ARCND1, ARCND2 and ARCND3) have been reported. To date, five pathogenic variants of GNAI3have been reported in ARCND1 patients. Here, we report a novel variant of GNAI3(NM_006496:c.807C>A:p.(Asn269Lys)) in a Japanese girl with micrognathia using trio-based whole exome sequencing analysis. The GNAI3gene encodes a heterotrimeric guanine nucleotide-binding protein. The novel variant locates the guanine nucleotide-binding site, and the substitution was predicted to interfere with guanine nucleotide-binding by in silico structural analysis. Three-dimensional computer tomography scan, or cephalogram, displayed severely hypoplastic mandibular rami and fusion to the medial and lateral pterygoid plates, which have been recognised in other ARCND1 patients, but have not been described in ARCND2 and ARCND3, suggesting that these may be distinguishable features in ARCND1.

Published
2021
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35. Fetal Therapy Model of Myelomeningocele with Three-Dimensional Skin Using Amniotic Fluid Cell-Derived Induced Pluripotent Stem Cells

Author

Kajiwara, Kazuhiro, primary, Tanemoto, Tomohiro, additional, Wada, Seiji, additional, Karibe, Jurii, additional, Ihara, Norimasa, additional, Ikemoto, Yu, additional, Kawasaki, Tomoyuki, additional, Oishi, Yoshie, additional, Samura, Osamu, additional, Okamura, Kohji, additional, Takada, Shuji, additional, Akutsu, Hidenori, additional, Sago, Haruhiko, additional, Okamoto, Aikou, additional, and Umezawa, Akihiro, additional

Published
2017
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45. ZNF384 -related fusion genes define a subgroup of childhood B-cell precursor acute lymphoblastic leukemia with a characteristic immunotype

Author

Hirabayashi, Shinsuke, primary, Ohki, Kentaro, additional, Nakabayashi, Kazuhiko, additional, Ichikawa, Hitoshi, additional, Momozawa, Yukihide, additional, Okamura, Kohji, additional, Yaguchi, Akinori, additional, Terada, Kazuki, additional, Saito, Yuya, additional, Yoshimi, Ai, additional, Ogata-Kawata, Hiroko, additional, Sakamoto, Hiromi, additional, Kato, Motohiro, additional, Fujimura, Junya, additional, Hino, Moeko, additional, Kinoshita, Akitoshi, additional, Kakuda, Harumi, additional, Kurosawa, Hidemitsu, additional, Kato, Keisuke, additional, Kajiwara, Ryosuke, additional, Moriwaki, Koichi, additional, Morimoto, Tsuyoshi, additional, Nakamura, Kozue, additional, Noguchi, Yasushi, additional, Osumi, Tomoo, additional, Sakashita, Kazuo, additional, Takita, Junko, additional, Yuza, Yuki, additional, Matsuda, Koich, additional, Yoshida, Teruhiko, additional, Matsumoto, Kenji, additional, Hata, Kenichiro, additional, Kubo, Michiaki, additional, Matsubara, Yoichi, additional, Fukushima, Takashi, additional, Koh, Katsuyoshi, additional, Manabe, Atsushi, additional, Ohara, Akira, additional, and Kiyokawa, Nobutaka, additional

Published
2016
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47. Complex Genomic Rearrangement Within theGNASRegion Associated With Familial Pseudohypoparathyroidism Type 1b

Author

Nakamura, Akie, primary, Hamaguchi, Erika, additional, Horikawa, Reiko, additional, Nishimura, Yasuyuki, additional, Matsubara, Keiko, additional, Sano, Shinichiro, additional, Nagasaki, Keisuke, additional, Matsubara, Yoichi, additional, Umezawa, Akihiro, additional, Tajima, Toshihiro, additional, Ogata, Tsutomu, additional, Kagami, Masayo, additional, Okamura, Kohji, additional, and Fukami, Maki, additional

Published
2016
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48. Distinctive features of single nucleotide alterations in induced pluripotent stem cells with different types of DNA repair deficiency disorders

Author

Okamura, Kohji, primary, Sakaguchi, Hironari, additional, Sakamoto-Abutani, Rie, additional, Nakanishi, Mahito, additional, Nishimura, Ken, additional, Yamazaki-Inoue, Mayu, additional, Ohtaka, Manami, additional, Periasamy, Vaiyapuri Subbarayan, additional, Alshatwi, Ali Abdullah, additional, Higuchi, Akon, additional, Hanaoka, Kazunori, additional, Nakabayashi, Kazuhiko, additional, Takada, Shuji, additional, Hata, Kenichiro, additional, Toyoda, Masashi, additional, and Umezawa, Akihiro, additional

Published
2016
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