The C. elegans Integrator complex controls the termination of piRNA transcription

piRNAs are a class of 21-30nt small RNAs enriched in the germline of metazoans that are essential for germline development and genome defence due to their ability to target transposable elements for silencing. In the nematode Caenorhabditis elegans, piRNAs are extremely short transcriptional units that generate 28nt short capped piRNA precursors. The mechanisms controlling premature termination of Pol II resulting in the biogenesis of short capped RNAs are poorly understood. In this work, we describe a role for Integrator, a metazoan-specific transcription termination complex in piRNA biogenesis. We show that Integrator cleavage of nascent piRNA transcripts is required for efficient generation of short piRNA precursors and mature piRNAs, and results in premature termination of promoter-proximal Pol II. Our work thus expands the range of non-coding RNA transcripts under Integrator control, and describes a role for Integrator in the termination of promoter-proximal Pol II.