title: Proposing a new RNA quadruplex structure: j-motif, with possible links to neural development.
abstract: An RNA-binding protein, hnRNP K, has been studied extensively because of its involvement in neural development through the post-transcriptional regulation of its downstream target genes; however, its binding mode remains unclear. According to structural features of the binding sites, we have presumed the existence of possible unique structures 'j-motifs' that are similar to known i-motifs, the difference being that the initial cluster comprises successive U nucleic acids instead of C. It was suspected that the motifs could be recognized by hnRNP K to regulate the translation levels of target proteins, however, there were virtually no methods to verify their existence except computational methods: regular expression searches and theoretical molecular orbital (MO) calculations. Here, we first show a list of 16 genes having j-motif-like sequences we discovered under refined search conditions. The list was highly related to neural development from both subjective and objective aspects. Additionally, MO calculations revealed the similarity of non-canonical base pairs found in i- and j-motifs qualitatively, leading to a proposal of the possible existence of the j-motifs. When taken into consideration, it was indicated that the j-motifs could be formed and play some role in the neural development.
authors.affiliation: Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555; Department of Physiology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582; Department of Science and Technology, Sophia University,7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554; and Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishishinbashi, Minato-ku, Tokyo, 105-8461, Japan shingo.nakamura@catalent.com hidokano@a2.keio.jp.
authors.forename: Shingo
authors.initials: S
authors.lastname: Nakamura
authors.affiliation: Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555; Department of Physiology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582; Department of Science and Technology, Sophia University,7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554; and Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishishinbashi, Minato-ku, Tokyo, 105-8461, JapanPharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555; Department of Physiology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582; Department of Science and Technology, Sophia University,7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554; and Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishishinbashi, Minato-ku, Tokyo, 105-8461, Japan hidokano@a2.keio.jp.
authors.forename: Mana
authors.initials: M
authors.lastname: Igarashi
authors.affiliation: Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555; Department of Physiology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582; Department of Science and Technology, Sophia University,7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554; and Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishishinbashi, Minato-ku, Tokyo, 105-8461, Japan.
authors.forename: Mika
authors.initials: M
authors.lastname: Kinoshita
authors.affiliation: Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555; Department of Physiology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582; Department of Science and Technology, Sophia University,7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554; and Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishishinbashi, Minato-ku, Tokyo, 105-8461, Japan.
authors.forename: Hirotaka J
authors.initials: HJ
authors.lastname: Okano
authors.affiliation: Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555; Department of Physiology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582; Department of Science and Technology, Sophia University,7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554; and Division of Regenerative Medicine, Jikei University School of Medicine, 3-25-8 Nishishinbashi, Minato-ku, Tokyo, 105-8461, Japan shingo.nakamura@catalent.com hidokano@a2.keio.jp.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Okano
mesh_terms: D000818:Animals; D020029:Base Pairing; D050759:Cyclin-Dependent Kinase Inhibitor p21 / Q000235:genetics; D015870:Gene Expression; D034641:Heterogeneous-Nuclear Ribonucleoprotein K / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry
chemical_list: C493957:Cdkn1a protein, mouse; D050759:Cyclin-Dependent Kinase Inhibitor p21; D034641:Heterogeneous-Nuclear Ribonucleoprotein K; D012333:RNA, Messenger; D012313:RNA
keywords: CDKN1A; MO calculation; hnRNP K; i-motif; regular expression search