Proposing a new RNA quadruplex structure: J-motif, with possible links to neural development

Shingo Nakamura, Mana Igarashi, Mika Kinoshita, Hirotaka J. Okano, Hideyuki Okano

Research output: Contribution to journalArticle

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.

Original languageEnglish
Pages (from-to)385-392
Number of pages8
JournalJournal of biochemistry
Volume155
Issue number6
DOIs
Publication statusPublished - 2014 Jun

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Keywords

  • CDKN1A
  • MO calculation
  • hnRNP K
  • i-motif
  • regular expression search

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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