R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants

GONZALO LUCÍA; TOSSOLINI ILEANA; GULANICZ TOMASZ; CAMBIAGNO DAMIAN ALEJANDRO; KASPROWICZ-MALUSKI ANNA; SMOLINSKI DARIUSZ JAN ; MAMMARELLA MARIA FLORENCIA; ARIEL FEDERICO ALEJANDRO; MARQUARDT SEBASTIAN; SZWEYKOWSKA-KULINSKA ZOFIA ; JARMOLOWSKI ARTUR; MANAVELLA PABLO ANDRÉS

Nature Plants

Palgrave Macmillan Ltd.

Año: 2022 vol. 8 p. 402 - 418

In most organisms, the maturation of nascent RNAs is coupled to transcription. Unlike in animals, the RNA polymerase II(RNAPII) transcribes microRNA genes (MIRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, itis unknown whether miRNA processing occurs co-transcriptionally. Here, we used native elongating transcript sequencing dataand imaging techniques to demonstrate that plant miRNA biogenesis occurs coupled to transcription. We found that the entirebiogenesis occurs co-transcriptionally for pri-miRNAs processed from the loop of the hairpin but requires a second nucleoplasmic step for those processed from the base. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops, formed near the transcription startsite region of MIRNAs, promote co-transcriptional pri-miRNA processing. Furthermore, our results suggest the neofunctionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.