Lumi Negishi

The GSEC-encoded polypeptide GESP drives colorectal cancer tumorigenesis via NPM1-c-Myc-mediated repression of NDRG1

Yoshihiro Kawasaki, Tomoatsu Hayashi, Akane Kitta-Kunihiro, Lumi Negishi et autres

Expression of long non-coding RNAs (lncRNAs) is frequently dysregulated in human cancers. We previously reported that the lncRNA GSEC accelerates colorectal cancer (CRC) cell motility by inhibiting the RNA helicase DHX36. Here, we demonstrated that a nuclear polypeptide (designated 'GESP') is translated …

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Structural basis of nucleosome remodeling by Cockayne syndrome B homologue Komagataella phaffii Rad26

Yutaro Fukushima, Chiaki Kinoshita, Lumi Negishi, Tomoya Kujirai et autres

Rad26, a yeast homologue of mammalian Cockayne syndrome protein B (CSB), plays an essential role in transcription-coupled nucleotide excision repair (TC-NER). Rad26/CSB binds RNA polymerase II stalled at DNA lesions and recruits DNA repair factors, functioning as a molecular scaffold. In addition, …

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Correction to: Quantitative Proteomic Profiling of Pinctada fucata Shell Nacre Defines a Solubility-Based Type Classification of Shell Matrix Proteins

Keisuke Oshima, Lumi Negishi, Takashi Atsumi, Hitoshi Atsumi et autres

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Identification, functional characterization, and cryo‐ EM structural analysis of novel ferritin subunits in Turbo sazae

Yuto Namikawa, Lumi Negishi, Hitoshi Kurumizaka, Michio Suzuki

Turbo sazae, an edible gastropod, accumulates high levels of iron in its digestive gland, and the molecular mechanism underlying this accumulation has remained elusive. This study identified the proteins responsible for the iron accumulation and characterized their function and structure. We isolated …

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Quantitative Proteomic Profiling of Pinctada fucata Shell Nacre Defines a Solubility-Based Type Classification of Shell Matrix Proteins

Keisuke Oshima, Lumi Negishi, Takashi Atsumi, Hitoshi Kurumizaka et autres

Shell matrix proteins (SMPs) are key organic components of molluscan biominerals, yet previous nacre proteomics have remained largely qualitative, limiting evaluation of the abundance and fraction association of individual SMPs. Here, we established a quantitative proteomic approach for the nacreous layer of …

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Zinc accumulation in the jaw of Nereis aibuhitensis

Yugo Kato, Wataru Kashiwabara, Mayumi Iijima, Keisuke Shimizu et autres

Zinc accumulates in the jaws of green worms, Nereis aibuhitensis, a phylum of annelid worms, to enhance the mechanical properties of the jaws for predation and migration. In this study, we precisely mapped the localization of zinc and identified the matrix proteins …

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myCRP, Cysteine-Rich Protein in the Yesso Scallop Mizuhopecten yessoensis, Is a Novel High-Molecular Weight Cd-Binding Protein

Zehua Zheng, Yuto Namikawa, Masahiko AWAJI, Yugo Kato et autres

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Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome

S. Matsumoto, Yoshimasa Takizawa, Mitsuo Ogasawara, Kana Hashimoto et autres

In mammalian global genomic nucleotide excision repair, UV-DDB plays a central role in recognizing DNA lesions, such as 6-4 photoproducts and cyclobutane pyrimidine dimers, within chromatin. In the present study, we perform cryo-electron microscopy analyses coupled with chromatin-immunoprecipitation to reveal that the …

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Exploring cadmium-binding proteins in Japanese scallops Mizuhopecten yessoensis: isolation and characterization

Zehua Zheng, Yuto Namikawa, Yugo Kato, Peng Lü et autres

Scallops (Mizuhopecten yessoensis) accumulate abnormal levels of cadmium (Cd) in their bodies; however, the chemical form of Cd in vivo remains unclear. In this study, Cd concentrations in various scallop tissues were measured, revealing that Cd predominantly accumulated as a water-soluble component …

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The Gln-rich protein twip1 promotes high-density {110} twins formation in the shell of the limpet Cellana rota

Sicheng Li, Zehua Zheng, Keisuke Oshima, Lingxiao Zhu et autres

Aragonite, a polymorph of calcium carbonate (CaCO 3 ), exhibits enhanced mechanical properties due to crystal defects such as twins, which are particularly prevalent in biogenic aragonite and can inhibit crack propagation. Despite the importance, the molecular mechanisms responsible for the formation …

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Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis

Tomoya Kujirai, Junko Katô, Kyoka Yamamoto, Seiya Hirai et autres

RNA polymerase II (RNAPII) is a central transcription enzyme that exists as multiple forms with or without accessory factors, and transcribes the genomic DNA packaged in chromatin. To understand how RNAPII functions in the human genome, we isolate transcribing RNAPII complexes from …

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Cryo‐ EM Structures of Native Chromatin Units From Human Cells

Suguru Hatazawa, Yoshiyuki Fukuda, Yuki Kobayashi, Lumi Negishi et autres

In eukaryotic cells, genomic DNA is compacted by nucleosomes, as basic repeating units, into chromatin. The nucleosome arrangement in chromatin fibers could be an important determinant for chromatin folding, by which genomic DNA is regulated in the nucleus. To study the structures …

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