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Decoding the 5′ nucleotide bias of PIWI-interacting RNAs

Author

Listed:
  • Chad B. Stein

    (National Institutes of Health
    Harvard Medical School)

  • Pavol Genzor

    (National Institutes of Health)

  • Sanga Mitra

    (National Institutes of Health)

  • Alexandra R. Elchert

    (National Institutes of Health)

  • Jonathan J. Ipsaro

    (Howard Hughes Medical Institute
    Cold Spring Harbor Laboratory)

  • Leif Benner

    (National Institutes of Health
    Johns Hopkins University)

  • Sushil Sobti

    (National Institutes of Health)

  • Yijun Su

    (National Institutes of Health)

  • Molly Hammell

    (Cold Spring Harbor Laboratory)

  • Leemor Joshua-Tor

    (Howard Hughes Medical Institute
    Cold Spring Harbor Laboratory)

  • Astrid D. Haase

    (National Institutes of Health)

Abstract

PIWI-interacting RNAs (piRNAs) are at the center of a small RNA-based immune system that defends genomes against the deleterious action of mobile genetic elements (transposons). PiRNAs are highly variable in sequence with extensive targeting potential. Their diversity is restricted by their preference to start with a Uridine (U) at the 5′ most position (1U-bias), a bias that remains poorly understood. Here we uncover that the 1U-bias of Piwi-piRNAs is established by consecutive discrimination against all nucleotides but U, first during piRNA biogenesis and then upon interaction with Piwi’s specificity loop. Sequence preferences during piRNA processing also restrict U across the piRNA body with the potential to directly impact target recognition. Overall, the uncovered signatures could modulate specificity and efficacy of piRNA-mediated transposon restriction, and provide a substrate for purifying selection in the ongoing arms race between genomes and their mobile parasites.

Suggested Citation

  • Chad B. Stein & Pavol Genzor & Sanga Mitra & Alexandra R. Elchert & Jonathan J. Ipsaro & Leif Benner & Sushil Sobti & Yijun Su & Molly Hammell & Leemor Joshua-Tor & Astrid D. Haase, 2019. "Decoding the 5′ nucleotide bias of PIWI-interacting RNAs," Nature Communications, Nature, vol. 10(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-08803-z
    DOI: 10.1038/s41467-019-08803-z
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    Cited by:

    1. Susanne Bornelöv & Benjamin Czech & Gregory J. Hannon, 2022. "An evolutionarily conserved stop codon enrichment at the 5′ ends of mammalian piRNAs," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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