Circular Concatemers of Ultra-Short DNA Segments Produce Regulatory RNAs

Summary In the ciliated protozoan Paramecium tetraurelia, Piwi-associated small RNAs are generated upon the elimination of tens of thousands of short transposon-derived DNA segments as part of development. These RNAs then target complementary DNA for elimination in a positive feedback process, contributing to germline defense and genome stability. In this work, we investigate the formation of these RNAs, which we show to be transcribed directly from the short (length mode 27 bp) excised DNA segments. Our data support a mechanism whereby the concatenation and circularization of excised DNA segments provides a template for RNA production. This process allows the generation of a double-stranded RNA for Dicer-like protein cleavage to give rise to a population of small regulatory RNAs that precisely match the excised DNA sequences. Video Abstract
Graphical Abstract
Highlights • In Paramecium, pieces of deleted DNA are transcribed to form regulatory RNAs • Ultra-short DNA segments are concatenated and circularized, allowing transcription • This concatenation is carried out by Ligase IV, which also repairs DNA ends • Concatenation is random, which leads to diversity in the resulting sRNA population
“Junk” DNA can be ligated into circles and transcribed to generate regulatory RNAs.