Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

Filippo M. Cernilogar, Maria Cristina Onorati, Greg O. Kothe, A. Maxwell Burroughs, Krishna Mohan Parsi, Achim Breiling, Federica Lo Sardo, Alka Saxena, Keita Miyoshi, Haruhiko Siomi, Mikiko C. Siomi, Piero Carninci, David S. Gilmour, Davide F V Corona, Valerio Orlando

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Pages (from-to)391-395
Number of pages5
JournalNature
Volume480
Issue number7377
DOIs
Publication statusPublished - 2011 Dec 15

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Small Nuclear RNA
RNA Interference
Drosophila
RNA Polymerase II
RNA
Shock
Hot Temperature
Chromatin
Antisense DNA
High-Throughput Nucleotide Sequencing
Genetic Loci
Heterochromatin
Gene Silencing
Missense Mutation
Transcriptome
Genetic Promoter Regions
Epigenomics
Cytoplasm
Nucleotides
Gene Expression

ASJC Scopus subject areas

  • General

Cite this

Cernilogar, F. M., Onorati, M. C., Kothe, G. O., Burroughs, A. M., Parsi, K. M., Breiling, A., ... Orlando, V. (2011). Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature, 480(7377), 391-395. https://doi.org/10.1038/nature10492

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. / Cernilogar, Filippo M.; Onorati, Maria Cristina; Kothe, Greg O.; Burroughs, A. Maxwell; Parsi, Krishna Mohan; Breiling, Achim; Sardo, Federica Lo; Saxena, Alka; Miyoshi, Keita; Siomi, Haruhiko; Siomi, Mikiko C.; Carninci, Piero; Gilmour, David S.; Corona, Davide F V; Orlando, Valerio.

In: Nature, Vol. 480, No. 7377, 15.12.2011, p. 391-395.

Research output: Contribution to journalArticle

Cernilogar, FM, Onorati, MC, Kothe, GO, Burroughs, AM, Parsi, KM, Breiling, A, Sardo, FL, Saxena, A, Miyoshi, K, Siomi, H, Siomi, MC, Carninci, P, Gilmour, DS, Corona, DFV & Orlando, V 2011, 'Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila', Nature, vol. 480, no. 7377, pp. 391-395. https://doi.org/10.1038/nature10492
Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A et al. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature. 2011 Dec 15;480(7377):391-395. https://doi.org/10.1038/nature10492
Cernilogar, Filippo M. ; Onorati, Maria Cristina ; Kothe, Greg O. ; Burroughs, A. Maxwell ; Parsi, Krishna Mohan ; Breiling, Achim ; Sardo, Federica Lo ; Saxena, Alka ; Miyoshi, Keita ; Siomi, Haruhiko ; Siomi, Mikiko C. ; Carninci, Piero ; Gilmour, David S. ; Corona, Davide F V ; Orlando, Valerio. / Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. In: Nature. 2011 ; Vol. 480, No. 7377. pp. 391-395.
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