title: Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila.
abstract: RNA interference (RNAi) pathways have evolved as important modulators of gene expression that operate in the cytoplasm by degrading RNA target molecules through the activity of short (21-30 nucleotide) RNAs. RNAi components have been reported to have a role in the nucleus, as they are involved in epigenetic regulation and heterochromatin formation. However, although RNAi-mediated post-transcriptional gene silencing is well documented, the mechanisms of RNAi-mediated transcriptional gene silencing and, in particular, the role of RNAi components in chromatin dynamics, especially in animal multicellular organisms, are elusive. Here we show that the key RNAi components Dicer 2 (DCR2) and Argonaute 2 (AGO2) associate with chromatin (with a strong preference for euchromatic, transcriptionally active, loci) and interact with the core transcription machinery. Notably, loss of function of DCR2 or AGO2 showed that transcriptional defects are accompanied by the perturbation of RNA polymerase II positioning on promoters. Furthermore, after heat shock, both Dcr2 and Ago2 null mutations, as well as missense mutations that compromise the RNAi activity, impaired the global dynamics of RNA polymerase II. Finally, the deep sequencing of the AGO2-associated small RNAs (AGO2 RIP-seq) revealed that AGO2 is strongly enriched in small RNAs that encompass the promoter regions and other regions of heat-shock and other genetic loci on both the sense and antisense DNA strands, but with a strong bias for the antisense strand, particularly after heat shock. Taken together, our results show that DCR2 and AGO2 are globally associated with transcriptionally active loci and may have a pivotal role in shaping the transcriptome by controlling the processivity of RNA polymerase II.
authors: Dulbecco Telethon Institute, Epigenetics and Genome Reprogramming, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy.
authors: Filippo M
authors: FM
authors: Cernilogar
authors: Maria Cristina
authors: MC
authors: Onorati
authors: Greg O
authors: GO
authors: Kothe
authors: A Maxwell
authors: AM
authors: Burroughs
authors: Krishna Mohan
authors: KM
authors: Parsi
authors: Achim
authors: A
authors: Breiling
authors: Federica
authors: F
authors: Lo Sardo
authors: Alka
authors: A
authors: Saxena
authors: Keita
authors: K
authors: Miyoshi
authors: Haruhiko
authors: H
authors: Siomi
authors: Mikiko C
authors: MC
authors: Siomi
authors: Piero
authors: P
authors: Carninci
authors: David S
authors: DS
authors: Gilmour
authors: Davide F V
authors: DF
authors: Corona
authors: Valerio
authors: V
authors: Orlando
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D029721:Drosophila Proteins / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000235:genetics*; D005786:Gene Expression Regulation; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics; D018869:Heat-Shock Response / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D020365:RNA Helicases / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D034622:RNA Interference; D012319:RNA Polymerase II / Q000378:metabolism; D012330:RNA, Double-Stranded / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D043244:Ribonuclease III / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors; D014158:Transcription, Genetic
chemical_list: C433807:AGO2 protein, Drosophila; D060565:Argonaute Proteins; D002843:Chromatin; D029721:Drosophila Proteins; D018840:HSP70 Heat-Shock Proteins; D035683:MicroRNAs; D012330:RNA, Double-Stranded; D016601:RNA-Binding Proteins; D014157:Transcription Factors; C118437:negative elongation factor; C478069:DCR-2 protein, Drosophila; D012319:RNA Polymerase II; D043244:Ribonuclease III; D020365:RNA Helicases