A Tetrahymena Piwi Bound to Mature tRNA 3' Fragments Activates the Exonuclease Xrn2 for RNA Processing in the Nucleus

Emerging evidence suggests that Ago/Piwi proteins function in the nucleus as well as the cytoplasm to control gene expression, but the mechanisms they employ in the nucleus remain poorly defined. The Tetrahymena thermophila Ago/Piwi protein Twi12 is essential for growth and functions in the nucleus. We show that Twi12 interacts with the exonuclease Xrn2. Twi12 functions to stabilize and localize Xrn2 in vivo, as well as activate its exonuclease activity in vitro. When Twi12 or Xrn2 are depleted, pre-rRNA processing intermediates accumulate and mature rRNA levels decline. RNA polymerase I and II (RNAP I and II) transcripts also accumulate. Twi12 function depends on small RNA (sRNA) binding, which is required for its nuclear import. Twi12-bound sRNAs are Dicer-independent 3' tRNA fragments that we propose may not be involved in sequence-specific base pairing to targets. Our findings suggest a role for tRNA fragments and an Ago/Piwi protein in global control of gene expression through interaction with a conserved exonuclease. Overall design: One library is analyzed here: small RNAs associated with ZZF-tagged Twi12. Twi12 is the full-length version, which is extended by 17 amino acids at the N-terminus compared to the previously-reported Twi12. Specifically, the 16-22 nt reads were analyzed here.