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Genes to Cells: Devoted to Molecular & Cellular Mechanisms

Andrew G Matveenko, Polina B Drozdova, Mikhail V Belousov, Svetlana E Moskalenko, Stanislav A Bondarev, Yury A Barbitoff, Anton A Nizhnikov, Galina A Zhouravleva
[PSI(+) ] is the prion form of the translation termination factor Sup35 (eRF3); [PSI(+) ] strains display nonsense suppression. Another prion-like element, [ISP(+) ], is linked to antisuppression in a specific background. Transcriptional regulator Sfp1 was shown to be responsible for [ISP(+) ] propagation. In this work, we identified SFP1 as a multicopy inducer of [PSI(+) ]-dependent lethality. Sfp1 is likely to up-regulate transcription of genes encoding release factors; however, its overproduction increases Sup35, but not Sup45 protein level...
October 12, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Atsuko Miki, Josephine Galipon, Satoshi Sawai, Toshifumi Inada, Kunihiro Ohta
Antisense RNA has emerged as a crucial regulator of opposite-strand protein-coding genes in the long noncoding RNA (lncRNA) category, but little is known about their dynamics and decay process in the context of a stress response. Antisense transcripts from the fission yeast fbp1 locus (fbp1-as) are expressed in glucose-rich conditions and anticorrelated with transcription of metabolic stress-induced lncRNA (mlonRNA) and mRNA on the sense strand during glucose starvation. Here, we investigate the localization and decay of antisense RNAs at fbp1 and other loci, and propose a model to explain the rapid switch between antisense and sense mlonRNA/mRNA transcription triggered by glucose starvation...
October 10, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Fumiki Katsuoka, Hiromi Yamazaki, Masayuki Yamamoto
Nrf1 and Nrf2 (NF-E2-related factors 1 and 2, respectively) are transcription factors that belong to the Cap'n'collar (CNC) family and play critical roles in various tissues, including the liver. Liver-specific Nrf1 knockout mice show hepatic steatosis, accompanied by dysregulation of various metabolic genes. Nrf2 knockout mice show impairment in the induction of antioxidant and xenobiotic-metabolizing enzyme genes. Although it has been shown that small Maf (sMaf) proteins act as obligatory partners of CNC proteins, their precise contributions to the function of CNC proteins remain unclear especially in the context of adult liver functions...
October 10, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Momoko Isogai, Hidefumi Suzuki, Ryo Maeda, Taka-Aki Tamura
Although the majority of gene expression is driven by TATA-binding protein (TBP)-based transcription machinery, it has been reported that TBP-related factors (TRFs) are also involved in the regulation of gene expression. TBP-like protein (TLP), which is one of the TRFs and exhibits the highest affinity to TFIIA among known proteins, has recently been showed to have significant roles in gene regulation. However, how the level of TLP is maintained in vivo has remained unknown. In this study, we explored the mechanism by which TLP protein is turned over in vivo and the factor that maintains the amount of TLP...
October 3, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Hisaaki Shinohara, Takeshi Nagashima, Marilia I Cascalho, Tomohiro Kurosaki
TAK1 (MAP3K7) mediation of the IκB kinase (IKK) complex-nuclear factor-κB (NF-κB) pathway is crucial for the activation of immune response and to perpetuate inflammation. Although progress has been made to understand TAK1 function in the B-cell receptor (BCR) signaling, the physiological roles of TAK1 in B-cell development, particularly in the bone marrow (BM), remain elusive. Previous studies suggested that the IKK complex is required for the development of immunoglobulin light chain λ-positive B cells, but not for receptor editing...
October 3, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Ayumi Nagasawa-Masuda, Kenta Terai
Vasculogenesis is essential during early development to construct networks transporting oxygen, blood and nutrients. Tip and stalk cells are specialized endothelial cells involved in novel vessel formation because of their behavior such as sprouting as a leading cell and following tip cell. However, the spatiotemporal details determining the emergence of these cells are unknown. Here, we first show that the ERK activity in endothelial cells represents the precursor of tip and stalk cells for vasculogenesis in zebrafish...
October 3, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Hisato Kobayashi, Tasuku Koike, Akihiko Sakashita, Keisuke Tanaka, Soichiro Kumamoto, Tomohiro Kono
Whole-genome shotgun bisulfite sequencing (WG-SBS) is currently the most powerful tool available for understanding genomewide cytosine methylation with single-base resolution; however, the high sequencing cost limits its widespread application, particularly for mammalian genomes. We mapped high- to low-coverage SBS short reads of mouse and human female developing germ cells to consensus sequences of repetitive elements that were multiplied in the respective host genome. This mapping strategy effectively identified active and evolutionarily young retrotransposon subfamilies and centromeric satellite repeats that were resistant to DNA demethylation during the investigated progressive stages of germ cell development...
October 3, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Kensuke Ninomiya, Mutsuhito Ohno, Naoyuki Kataoka
Localization of mRNA in neuronal cells is a critical process for spatiotemporal regulation of gene expression. Cytoplasmic localization of mRNA is often conferred by transport elements in 3' untranslated region (UTR). Activity-regulated cytoskeleton-associated protein (arc) mRNA is one of the localizing mRNAs in neuronal cells, and its localization is mediated by dendritic targeting element (DTE). As arc mRNA has introns in its 3' UTR, it was thought that arc mRNA is a natural target of nonsense-mediated mRNA decay (NMD)...
September 23, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Tetsushi Sakuma, Keiichi Masaki, Hiromi Abe-Chayama, Keiji Mochida, Takashi Yamamoto, Kazuaki Chayama
CRISPR-Cas9-mediated genome-editing technology contributes not only to basic genomic studies but also to clinical studies such as genetic correction and virus inactivation. Hepatitis B virus (HBV) is a major target for potential application of CRISPR-Cas9 in eliminating viral DNA from human cells. However, the high stability of covalently closed circular DNA (cccDNA) makes it difficult to completely clear HBV infection. Here, we report highly multiplexed CRISPR-Cas9-nuclease and Cas9-nickase vector systems that simultaneously target three critical domains of the HBV genome...
September 23, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
La Ode Muhammad Muchdar Davis, Nobuo Ogita, Soichi Inagaki, Naoki Takahashi, Masaaki Umeda
Lateral roots (LRs) are an important organ for water and nutrient uptake from soil. Thus, control of LR formation is crucial in the adaptation of plant growth to environmental conditions. However, the underlying mechanism controlling LR formation in response to external factors has remained largely unknown. Here, we found that LR formation was inhibited by DNA damage. Treatment with zeocin, which causes DNA double-strand breaks, up-regulated several DNA repair genes in the LR primordium (LRP) through the signaling pathway mediated by the transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1)...
September 23, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Yayoi Takamoto, Yoshimi Arima, Hideyuki Saya
Phyllodes tumors (PTs) are rare fibroepithelial tumors of the breast with epithelial and stromal components, and surgical resection is the standard and only available treatment for malignant PTs. To provide a better understanding of these tumors, we developed mouse models that recapitulate the pathological and clinical properties of human malignant PTs. Mouse undifferentiated mammary gland cells were infected with a retrovirus encoding the human oncoprotein H-Ras(G12V) , and the infected cells were transplanted orthotopically into the mammary fat pads of syngeneic mice...
September 23, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Kazushiro Fujiwara, Koichi Hasegawa, Masahiro Oka, Yoshihiro Yoneda, Kazuaki Yoshikawa
Terminal differentiation of neurons is accompanied by irreversible exit from the cell cycle and expression of neuronal phenotypes. The molecular mechanism whereby committed neuronal progenitors lose their ability to reenter the cell cycle is largely unknown. Here, we report that the nuclear transport system is rapidly remodeled in primary cortical progenitor cells (CPCs) at the very beginning of neuronal terminal differentiation. High levels of Ran GTPase-activating protein 1 (RanGAP), a key regulator of the Ran GTP-GDP cycle, in primary CPCs are drastically reduced upon neuronal induction...
September 22, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Ryo Koyama, Tomoya Arai, Marie Kijima, Shoko Sato, Shigetoshi Miura, Makoto Yuasa, Daisuke Kitamura, Ryushin Mizuta
Serum endonucleases are essential for degrading the chromatin released from dead cells and preventing autoimmune diseases such as systemic lupus erythematosus. Serum DNase I is known as the major endonuclease, but recently, another endonuclease, DNase γ/DNase I-like 3, gained attention. However, the precise role of each endonuclease, especially that of DNase γ, remains unclear. In this study, we distinguished the activities of DNase γ from those of DNase I in mouse serum and concluded that both cooperated in degrading DNA during necrosis: DNase γ functions as the primary chromatolytic activity, causing internucleosomal DNA fragmentation, and DNase I as the secondary one, causing random DNA digestion for its complete degradation...
September 22, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Kazuma Kamata, Kaori Shinmyozu, Jun-Ichi Nakayama, Masanori Hatashita, Hiroyuki Uchida, Masaya Oki
In eukaryotic cells, there are two chromatin states, silenced and active, and the formation of a so-called boundary plays a critical role in demarcating these regions; however, the mechanisms underlying boundary formation are not well understood. In this study, we focused on S. cerevisiae ADA1, a gene previously shown to encode a protein with a robust boundary function. Ada1 is a component of the histone modification complex Spt-Ada-Gcn5-acetyltransferase (SAGA) and the SAGA-like (SLIK) complex, and it helps to maintain the integrity of these complexes...
October 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Masatoshi Takagi, Toyoaki Natsume, Masato T Kanemaki, Naoko Imamoto
Although the condensin complexes and topoisomerase IIα (TopoIIα) are the central players in mitotic chromosome formation, they are insufficient for its completion, and additional factors involved in the process have been extensively sought. In this study, we examined the possibility that Ki67, a perichromosomal protein widely used as a cell proliferation marker, is one such factor. Using a combination of auxin-inducible degron and CRISPR-Cas9-based gene editing technologies, we generated a human HCT116 cell line in which Ki67 is rapidly depleted in a few hours...
October 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Atsushi Hatano, Masaki Matsumoto, Keiichi I Nakayama
A key issue in the study of signal transduction is how multiple signaling pathways are systematically integrated into the cell. We have now performed multiple phosphoproteomics analyses focused on the dynamics of the T-cell receptor (TCR) signaling network and its subsystem mediated by the Ca(2+) signaling pathway. Integration of these phosphoproteomics data sets and extraction of components of the TCR signaling network dependent on Ca(2+) signaling showed unexpected phosphorylation kinetics for candidate substrates of the Ca(2+) -dependent phosphatase calcineurin (CN) during TCR stimulation...
October 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Govinda Sharma, Koji Tsutsumi, Taro Saito, Akiko Asada, Kanae Ando, Mineko Tomomura, Shin-Ichi Hisanaga
Neurite formation, a fundamental process in neuronal maturation, requires the coordinated regulation of cytoskeletal reorganization and membrane transport. Compared to the understanding of cytoskeletal functions, less is known about the supply of membranes to growing neurites. Lemur kinase 1A (LMTK1A) is an endosomal protein kinase that is highly expressed in neurons. We recently reported that LMTK1A regulates the trafficking of Rab11-positive recycling endosomes in growing axons and dendrites. Here, we used the kinase-negative (kn) mutant to investigate the role of the kinase activity of LMTK1A in its cellular localization and interactions with the cytoskeleton in Neuro2A and PC-12 cells...
October 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Haruko Nakamura, Naoya Yamashita, Ayuko Kimura, Yayoi Kimura, Hisashi Hirano, Hiroko Makihara, Yuko Kawamoto, Aoi Jitsuki-Takahashi, Kumiko Yonezaki, Kenkichi Takase, Tomoyuki Miyazaki, Fumio Nakamura, Fumiaki Tanaka, Yoshio Goshima
Collapsin response mediator protein 2 (CRMP2) plays a key role in axon guidance, dendritic morphogenesis and cell polarization. CRMP2 is implicated in various neurological and psychiatric disorders. However, in vivo functions of CRMP2 remain unknown. We generated CRMP2 gene-deficient (crmp2(-/-) ) mice and examined their behavioral phenotypes. During 24-h home cage monitoring, the activity level during the dark phase of crmp2(-/-) mice was significantly higher than that of wild-type (WT) mice. Moreover, the time during the open arm of an elevated plus maze was longer for crmp2(-/-) mice than for WT mice...
October 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Kaito Yoza, Rika Himeno, Shinjiro Amano, Yoshihiro Kobashigawa, Shun Amemiya, Natsuki Fukuda, Hiroyuki Kumeta, Hiroshi Morioka, Fuyuhiko Inagaki
Over-expression and aberrant activation of tyrosine kinases occur frequently in human cancers. Various tyrosine kinase inhibitors (TKIs) are under clinical use, but acquisition of resistance to these drugs is a major problem. Here, we studied the interaction between two drug-resistant mutants of fibroblast growth factor receptor 1 (FGFR1), N546K and V561M, and four ATP-competitive inhibitors, ponatinib, dovitinib, PD173074 and BGJ-398. Among these protein-drug systems, the only marked reduction in affinity was that of PD173074 for the V561M mutant...
October 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Kumiko Torisu, Xueli Zhang, Mari Nonaka, Takahide Kaji, Daisuke Tsuchimoto, Kosuke Kajitani, Kunihiko Sakumi, Takehiro Torisu, Kazuhiro Chida, Katsuo Sueishi, Michiaki Kubo, Jun Hata, Takanari Kitazono, Yutaka Kiyohara, Yusaku Nakabeppu
Genomewide association studies have shown that a nonsynonymous single nucleotide polymorphism in PRKCH is associated with cerebral infarction and atherosclerosis-related complications. We examined the role of PKCη in lipid metabolism and atherosclerosis using apolipoprotein E-deficient (Apoe(-/-) ) mice. PKCη expression was augmented in the aortas of mice with atherosclerosis and exclusively detected in MOMA2-positive macrophages within atherosclerotic lesions. Prkch(+/+) Apoe(-/-) and Prkch(-/-) Apoe(-/-) mice were fed a high-fat diet (HFD), and the dyslipidemia observed in Prkch(+/+) Apoe(-/-) mice was improved in Prkch(-/-) Apoe(-/-) mice, with a particular reduction in serum LDL cholesterol and phospholipids...
October 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
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