Control of alternative splicing through siRNA-mediated transcriptional gene silencing

MARIANO ALLÓ1, VALERIA BUGGIANO1, JUAN P FEDEDA1, EZEQUIEL PETRILLO1, IGNACIO SCHOR1, MANUEL DE LA MATA1, ENERITZ AGIRRE2, MIREYA PLASS2, EDUARDO EYRAS2, SHERIF ABOU ELELA3, ROSCOE KLINCK3, BENOIT CHABOT3 & ALBERTO R KORNBLIHTT

NATURE STRUCTURAL & MOLECULAR BIOLOGY

NATURE PUBLISHING GROUP

Año: 2010 vol. 16 p. 717 - 724

1545-9985

When targeting promoter regions, small interfering RNAs (siRNAs) trigger a previously proposed pathway known as transcriptional gene silencing by promoting heterochromatin formation. Here we show that siRNAs targeting intronic or exonic sequences close to an alternative exon regulate the splicing of that exon. The effect occurred in hepatoma and HeLa cells with siRNA antisense strands designed to enter the silencing pathway, suggesting hybridization with nascent pre-mRNA. Unexpectedly, in HeLa cells the sense strands were also effective, suggesting that an endogenous antisense transcript, detectable in HeLa but not in hepatoma cells, acts as a target. The effect depends on Argonaute-1 and is counterbalanced by factors favoring chromatin opening or transcriptional elongation. The increase in heterochromatin marks (dimethylation at Lys9 and trimethylation at Lys27 of histone H3) at the target site, the need for the heterochromatin-associated protein HP1alpha and the reduction in RNA polymerase II processivity suggest a mechanism involving the kinetic coupling of transcription and alternative splicing.