siRNA-mediated epigenetic control of alternative splicing

MARIANO ALLÓ,1 VALERIA BUGGIANO,1 JUAN PABLO FEDEDA,1 EZEQUIEL PETRILLO,1 IGNACIO SCHOR,1 MANUEL DE LA MATA,1 ENERITZ AGIRRE,2 MIREYA PLASS,2 EDUARDO EYRAS,2 AND ALBERTO R. KORNBLIHTT

Oxford, UK

Congreso; Messenger RNA 3’ ends & gene expression; 2009

European Molecular Biology Organization

Small interfering RNAs (siRNAs) are known to mediate post-transcriptional gene silencing (PTGS) by promoting degradation of target mRNAs. When targeted at promoter regions, siRNAs participate in an alternative pathway known as transcriptional gene silencing (TGS) by promoting histone methylation, heterochromatin formation and inhibition of transcription. Here we show that siRNAs targeting sequences located close to an alternative exon are able to regulate its alternative pre-mRNA splicing in human cells. The effect needs both AGO-1 and AGO-2 and is abolished or reduced by factors that favor an open chromatin structure or increase transcriptional elongation. The mechanism involves the presence of facultative heterochromatin epigenetic marks (H3K9me2 and H3K27me3) at the target site and the hetorochromatin associated protein HP1 alpha. The effect is not only triggered by intronic but also by exonic siRNAs. The use of the cancer-related panel for alternative splicing in cells depleted of AGO1 and Dicer shed light on a possible endogenous pathway of this process. Moreover, we found significant differences in the upstream intron size of events affected by AGO1 knockdown relative to non-affected ones.