PIWI Slicing and EXD1 Drive Biogenesis of Nuclear piRNAs from Cytosolic Targets of the Mouse piRNA Pathway

Zhaolin Yang; Kuan-Ming Chen; Radha Raman Pandey; David Homolka; Michael Reuter; Bruno Kotska Rodino Janeiro; Ravi Sachidanandam; Marie-Odile Fauvarque; Andrew A McCarthy; Ramesh S Pillai

doi:10.1016/j.molcel.2015.11.009

PIWI Slicing and EXD1 Drive Biogenesis of Nuclear piRNAs from Cytosolic Targets of the Mouse piRNA Pathway

Mol Cell. 2016 Jan 7;61(1):138-52. doi: 10.1016/j.molcel.2015.11.009. Epub 2015 Dec 6.

Affiliations

¹ European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France.
² Department of Oncological Sciences, Icahn School of Medicine at Sinai, One Gustave L. Levy Place, NY 10029, USA.
³ iRTSV, CEA-Grenoble, 17, rue des Martyrs, 38054 Grenoble Cedex 9, France.
⁴ European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France. Electronic address: pillai@embl.fr.

Abstract

PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposons in the cytoplasm and nucleus of animal germ cells, but how silencing in the two compartments is coordinated is not known. Here we demonstrate that endonucleolytic slicing of a transcript by the cytosolic mouse PIWI protein MILI acts as a trigger to initiate its further 5'→3' processing into non-overlapping fragments. These fragments accumulate as new piRNAs within both cytosolic MILI and the nuclear MIWI2. We also identify Exonuclease domain-containing 1 (EXD1) as a partner of the MIWI2 piRNA biogenesis factor TDRD12. EXD1 homodimers are inactive as a nuclease but function as an RNA adaptor within a PET (PIWI-EXD1-Tdrd12) complex. Loss of Exd1 reduces sequences generated by MILI slicing, impacts biogenesis of MIWI2 piRNAs, and de-represses LINE1 retrotransposons. Thus, piRNA biogenesis triggered by PIWI slicing, and promoted by EXD1, ensures that the same guides instruct PIWI proteins in the nucleus and cytoplasm.

Keywords: Bombyx; Exd1; Inchworming; PIWI; Ping-pong; Slicer; Tdrd12; piRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Animals
Argonaute Proteins / chemistry
Argonaute Proteins / genetics
Argonaute Proteins / metabolism*
Carrier Proteins / metabolism
Cell Nucleus / enzymology*
Cytosol / enzymology*
Drosophila Proteins / genetics
Drosophila Proteins / metabolism
Drosophila melanogaster / genetics
Drosophila melanogaster / metabolism
Exonucleases / chemistry
Exonucleases / genetics
Exonucleases / metabolism*
Female
Gene Expression Regulation
Male
Mice, Transgenic
Models, Molecular
Molecular Sequence Data
Multiprotein Complexes
Protein Interaction Domains and Motifs
RNA Interference
RNA Processing, Post-Transcriptional*
RNA, Small Interfering / genetics
RNA, Small Interfering / metabolism*
RNA-Binding Proteins / chemistry
RNA-Binding Proteins / genetics
RNA-Binding Proteins / metabolism*

Substances

Argonaute Proteins
Carrier Proteins
Drosophila Proteins
EXD1 protein, mouse
Multiprotein Complexes
PIWIL4 protein, mouse
Piwil1 protein, mouse
Piwil2 protein, mouse
RNA, Small Interfering
RNA-Binding Proteins
piwi protein, Drosophila
tudor domain-containing protein 12, mouse
Exonucleases