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T-hairpin structure found in the RNA element involved in piRNA biogenesis

Naomi Takase1, Maina Otsu1, Shigeki Hirakata2

  • 1Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan.

RNA (New York, N.Y.)
|January 6, 2022
PubMed

Insights

PIWI-interacting RNAs (piRNAs) protect the genome by repressing transposons. Researchers discovered a novel T-hairpin structure in Drosophila Tj-cis RNA, crucial for piRNA biogenesis and Yb protein interaction.

Area of Science:

  • Molecular Biology
  • Genetics
  • RNA Biology

Background:

  • PIWI-interacting RNAs (piRNAs) are essential for germline genome integrity by suppressing transposable elements.
  • In Drosophila, piRNA production involves the 3'-untranslated region (3'-UTR) of the Traffic jam (Tj) mRNA, specifically a cis-acting element (Tj-cis).

Purpose of the Study:

  • To elucidate the structural basis of the Tj-cis RNA element's function in piRNA biogenesis.
  • To identify the structural features of Tj-cis RNA recognized by piRNA biogenesis factors.

Main Methods:

  • Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) and Nuclear Magnetic Resonance (NMR) spectroscopy were used to determine RNA structure.
  • piRNA biogenesis assays were performed to assess the functional importance of identified RNA structures.

Main Results:

  • SHAPE and NMR analyses revealed a stable hairpin structure in the 5' half of the 100-nt Tj-cis RNA.
  • A novel 16-nt stem-loop structure, termed the T-hairpin, was identified within this hairpin, featuring solvent-exposed uridine residues.
  • Both the T-hairpin and the 3' half of the Tj-cis RNA were found to be essential for piRNA biogenesis, indicating recognition by the Yb protein.

Conclusions:

  • The T-hairpin structure in Tj-cis RNA is a key determinant for piRNA biogenesis in Drosophila.
  • The exposed uridines in the T-hairpin likely serve as a binding site for the Yb protein, a Tudor domain-containing factor.
  • The functional requirement for both the T-hairpin and the 3' half suggests a complex interaction between Tj-cis RNA and Yb protein during piRNA production.
Keywords:
NMRRNA structure motifT-hairpinTj-cis elementYb proteinpiRNA biogenesis

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