Decoding the 5' nucleotide bias of PIWI-interacting RNAs

Stein, C. B., Genzor, P., Mitra, S., Elchert, A. R., Ipsaro, J. J., Benner, L., Sobti, S., Su, Y., Hammell, M., Joshua-Tor, L., Haase, A. D. (February 2019) Decoding the 5' nucleotide bias of PIWI-interacting RNAs. Nat Commun, 10 (1). p. 828. ISSN 2041-1723

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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.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification organism description > animal > insect > Drosophila bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > Piwi protein bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification organism description > animal bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > argonaute proteins organism description > animal > insect bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
CSHL Authors:	Ipsaro, Jonathan J. Hammell, Molly Joshua-Tor, Leemor
Communities:	CSHL labs > Hammell M. lab CSHL labs > Joshua-Tor lab CSHL Cancer Center Program > Cancer Genetics and Genomics Program CSHL Cancer Center Program > Gene Regulation and Inheritance Program
Depositing User:	Matthew Dunn
Date:	19 February 2019
Date Deposited:	22 Feb 2019 21:09
Last Modified:	02 Feb 2024 20:59
PMCID:	PMC6381166
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/37712

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