Article

Chromatin-associated RNAi components contribute to transcriptional regulation in Drosophila

Dulbecco Telethon Institute, Epigenetics and Genome Reprogramming, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy.
Nature (Impact Factor: 42.35). 11/2011; 480(7377):391-5. DOI: 10.1038/nature10492
Source: PubMed

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.

Download full-text

Full-text

Available from: Federica Lo Sardo, Aug 12, 2015
1 Follower
 · 
288 Views
  • Source
    • "Classically, these silencing pathways have been thought to act on heterochromatic repetitive elements, such as transposons, but more recently a broader role at euchromatic genes has been discovered. Studies in Arabidopsis (Liu et al., 2012), Drosophila (Cernilogar et al., 2011), C. elegans (Guang et al., 2010), and S. pombe (Gullerova et al., 2011; Gullerova and Proudfoot, 2008; Woolcock et al., 2012) have implicated nuclear small RNA pathways in the regulation of RNA Pol II (Pol II) at individual euchromatic genes. In fission yeast, this conserved function of RNAi (Pol II regulation) is particularly important in the context of DNA replication. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Nuclear RNAi is an important regulator of transcription and epigenetic modification, but the underlying mechanisms remain elusive. Using a genome-wide approach in the fission yeast S. pombe, we have found that Dcr1, but not other components of the canonical RNAi pathway, promotes the release of Pol II from the 3? end of highly transcribed genes, and, surprisingly, from antisense transcription of rRNA and tRNA genes, which are normally transcribed by Pol I and Pol III. These Dcr1-terminated loci correspond to sites of replication stress and DNA damage, likely resulting from transcription-replication collisions. At the rDNA loci, release of Pol II facilitates DNA replication and prevents homologous recombination, which would otherwise lead to loss of rDNA repeats especially during meiosis. Our results reveal a novel role for Dcr1-mediated transcription termination in genome maintenance and may account for widespread regulation of genome stability by nuclear RNAi in higher eukaryotes.
    Cell 10/2014; 159(3):572-83. DOI:10.1016/j.cell.2014.09.031 · 33.12 Impact Factor
  • Source
    • "SiRNA-directed recruitment of the nuclear RNAi components , the NRDE factors, could inhibit RNA Pol II during the elongation phase of transcription (Guang et al. 2010). A recent report suggests that the key protein components of the RNAi pathway, i.e., DCR2 and AGO2, could directly interact with the transcription machinery and control the processivity of RNA Pol II in Drosophila (Cernilogar et al. 2011). These findings raise the possibility that small noncoding RNAs could directly interact with the Pol II core transcription machinery and affect gene transcription in metazoans. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The TATA box represents one of the most prevalent core promoters where the pre-initiation complexes (PICs) for gene transcription are assembled. This assembly is crucial for transcription initiation and well regulated. Here we show that some cellular microRNAs (miRNAs) are associated with RNA polymerase II (Pol II) and TATA box-binding protein (TBP) in human peripheral blood mononuclear cells (PBMCs). Among them, let-7i sequence specifically binds to the TATA-box motif of interleukin-2 (IL-2) gene and elevates IL-2 mRNA and protein production in CD4+ T-lymphocytes in vitro and in vivo. Through direct interaction with the TATA-box motif, let-7i facilitates the PIC assembly and transcription initiation of IL-2 promoter. Several other cellular miRNAs, such as mir-138, mir-92a or mir-181d, also enhance the promoter activities via binding to the TATA-box motifs of insulin, calcitonin or c-myc, respectively. In agreement with the finding that an HIV-1–encoded miRNA could enhance viral replication through targeting the viral promoter TATA-box motif, our data demonstrate that the interaction with core transcription machinery is a novel mechanism for miRNAs to regulate gene expression.
    RNA 10/2014; · 4.62 Impact Factor
  • Source
    • "SiRNA-directed recruitment of the nuclear RNAi components , the NRDE factors, could inhibit RNA Pol II during the elongation phase of transcription (Guang et al. 2010). A recent report suggests that the key protein components of the RNAi pathway, i.e., DCR2 and AGO2, could directly interact with the transcription machinery and control the processivity of RNA Pol II in Drosophila (Cernilogar et al. 2011). These findings raise the possibility that small noncoding RNAs could directly interact with the Pol II core transcription machinery and affect gene transcription in metazoans. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The TATA box represents one of the most prevalent core promoters where the pre-initiation complexes (PICs) for gene transcription are assembled. This assembly is crucial for transcription initiation and well regulated. Here we show that some cellular microRNAs (miRNAs) are associated with RNA polymerase II (Pol II) and TATA box-binding protein (TBP) in human peripheral blood mononuclear cells (PBMCs). Among them, let-7i sequence specifically binds to the TATA-box motif of interleukin-2 (IL-2) gene and elevates IL-2 mRNA and protein production in CD4(+) T-lymphocytes in vitro and in vivo. Through direct interaction with the TATA-box motif, let-7i facilitates the PIC assembly and transcription initiation of IL-2 promoter. Several other cellular miRNAs, such as mir-138, mir-92a or mir-181d, also enhance the promoter activities via binding to the TATA-box motifs of insulin, calcitonin or c-myc, respectively. In agreement with the finding that an HIV-1-encoded miRNA could enhance viral replication through targeting the viral promoter TATA-box motif, our data demonstrate that the interaction with core transcription machinery is a novel mechanism for miRNAs to regulate gene expression.
    RNA 10/2014; 20(12). DOI:10.1261/rna.045633.114 · 4.62 Impact Factor
Show more