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Nuclear outsourcing of RNA interference components to human mitochondria.

Bandiera S, Rüberg S, Girard M, Cagnard N, Hanein S, Chrétien D, Munnich A, Lyonnet S, Henrion-Caude A - PLoS ONE (2011)

Bottom Line: We found 57 miRNAs differentially expressed in HeLa mitochondria and cytosol.Interestingly, the specificities of mitochondrial versus cytosolic miRNAs were underlined by significantly different structural and thermodynamic parameters.This study provides the first comprehensive view of the localization of RNA interference components to the mitochondria.

View Article: PubMed Central - PubMed

Affiliation: INSERM U781 Hôpital Necker-Enfants Malades, Paris, France.

ABSTRACT
MicroRNAs (miRNAs) are small non-coding RNAs that associate with Argonaute proteins to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in other cellular compartments. Mitochondria harbour their own genetic system that may be a potential site for miRNA mediated post-transcriptional regulation. We aimed at investigating whether nuclear-encoded miRNAs can localize to and function in human mitochondria. To enable identification of mitochondrial-enriched miRNAs, we profiled the mitochondrial and cytosolic RNA fractions from the same HeLa cells by miRNA microarray analysis. Mitochondria were purified using a combination of cell fractionation and immunoisolation, and assessed for the lack of protein and RNA contaminants. We found 57 miRNAs differentially expressed in HeLa mitochondria and cytosol. Of these 57, a signature of 13 nuclear-encoded miRNAs was reproducibly enriched in mitochondrial RNA and validated by RT-PCR for hsa-miR-494, hsa-miR-1275 and hsa-miR-1974. The significance of their mitochondrial localization was investigated by characterizing their genomic context, cross-species conservation and instrinsic features such as their size and thermodynamic parameters. Interestingly, the specificities of mitochondrial versus cytosolic miRNAs were underlined by significantly different structural and thermodynamic parameters. Computational targeting analysis of most mitochondrial miRNAs revealed not only nuclear but also mitochondrial-encoded targets. The functional relevance of miRNAs in mitochondria was supported by the finding of Argonaute 2 localization to mitochondria revealed by immunoblotting and confocal microscopy, and further validated by the co-immunoprecipitation of the mitochondrial transcript COX3. This study provides the first comprehensive view of the localization of RNA interference components to the mitochondria. Our data outline the molecular bases for a novel layer of crosstalk between nucleus and mitochondria through a specific subset of human miRNAs that we termed 'mitomiRs'.

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Integrative model for subcellular localization of RNAi components.Boxes represent the subcellular compartments. RNAi components are encircled. Arrows indicate the molecular fluxes documented herein in regards to the mitochondrial miRNAs (mitomiRs), and previously in P-bodies (PBs) [17], stress granules (SGs) [16], [54], multivesicular bodies (MVBs) [21] and Golgi [26]. Depending on the localization, different functions are ascribed to AGO2, such as post-transcriptional gene silencing or reversible translational regulation in P-bodies [50] and stress granules [16], and transcriptional regulation in the nucleus [51]. In mitochondria, the presence of mitochondrial genome adds another possible layer of regulation by AGO2.
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pone-0020746-g008: Integrative model for subcellular localization of RNAi components.Boxes represent the subcellular compartments. RNAi components are encircled. Arrows indicate the molecular fluxes documented herein in regards to the mitochondrial miRNAs (mitomiRs), and previously in P-bodies (PBs) [17], stress granules (SGs) [16], [54], multivesicular bodies (MVBs) [21] and Golgi [26]. Depending on the localization, different functions are ascribed to AGO2, such as post-transcriptional gene silencing or reversible translational regulation in P-bodies [50] and stress granules [16], and transcriptional regulation in the nucleus [51]. In mitochondria, the presence of mitochondrial genome adds another possible layer of regulation by AGO2.

Mentions: Little is known about the crosstalk between the nucleus and mitochondria, despite the fact that this communication has great relevance for understanding integrative cellular signaling pathways. In this report, we have used complementary approaches to provide evidence that all components of RNA interference are present at the mitochondria in human cells (Figure 8).


Nuclear outsourcing of RNA interference components to human mitochondria.

Bandiera S, Rüberg S, Girard M, Cagnard N, Hanein S, Chrétien D, Munnich A, Lyonnet S, Henrion-Caude A - PLoS ONE (2011)

Integrative model for subcellular localization of RNAi components.Boxes represent the subcellular compartments. RNAi components are encircled. Arrows indicate the molecular fluxes documented herein in regards to the mitochondrial miRNAs (mitomiRs), and previously in P-bodies (PBs) [17], stress granules (SGs) [16], [54], multivesicular bodies (MVBs) [21] and Golgi [26]. Depending on the localization, different functions are ascribed to AGO2, such as post-transcriptional gene silencing or reversible translational regulation in P-bodies [50] and stress granules [16], and transcriptional regulation in the nucleus [51]. In mitochondria, the presence of mitochondrial genome adds another possible layer of regulation by AGO2.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3113838&req=5

pone-0020746-g008: Integrative model for subcellular localization of RNAi components.Boxes represent the subcellular compartments. RNAi components are encircled. Arrows indicate the molecular fluxes documented herein in regards to the mitochondrial miRNAs (mitomiRs), and previously in P-bodies (PBs) [17], stress granules (SGs) [16], [54], multivesicular bodies (MVBs) [21] and Golgi [26]. Depending on the localization, different functions are ascribed to AGO2, such as post-transcriptional gene silencing or reversible translational regulation in P-bodies [50] and stress granules [16], and transcriptional regulation in the nucleus [51]. In mitochondria, the presence of mitochondrial genome adds another possible layer of regulation by AGO2.
Mentions: Little is known about the crosstalk between the nucleus and mitochondria, despite the fact that this communication has great relevance for understanding integrative cellular signaling pathways. In this report, we have used complementary approaches to provide evidence that all components of RNA interference are present at the mitochondria in human cells (Figure 8).

Bottom Line: We found 57 miRNAs differentially expressed in HeLa mitochondria and cytosol.Interestingly, the specificities of mitochondrial versus cytosolic miRNAs were underlined by significantly different structural and thermodynamic parameters.This study provides the first comprehensive view of the localization of RNA interference components to the mitochondria.

View Article: PubMed Central - PubMed

Affiliation: INSERM U781 Hôpital Necker-Enfants Malades, Paris, France.

ABSTRACT
MicroRNAs (miRNAs) are small non-coding RNAs that associate with Argonaute proteins to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in other cellular compartments. Mitochondria harbour their own genetic system that may be a potential site for miRNA mediated post-transcriptional regulation. We aimed at investigating whether nuclear-encoded miRNAs can localize to and function in human mitochondria. To enable identification of mitochondrial-enriched miRNAs, we profiled the mitochondrial and cytosolic RNA fractions from the same HeLa cells by miRNA microarray analysis. Mitochondria were purified using a combination of cell fractionation and immunoisolation, and assessed for the lack of protein and RNA contaminants. We found 57 miRNAs differentially expressed in HeLa mitochondria and cytosol. Of these 57, a signature of 13 nuclear-encoded miRNAs was reproducibly enriched in mitochondrial RNA and validated by RT-PCR for hsa-miR-494, hsa-miR-1275 and hsa-miR-1974. The significance of their mitochondrial localization was investigated by characterizing their genomic context, cross-species conservation and instrinsic features such as their size and thermodynamic parameters. Interestingly, the specificities of mitochondrial versus cytosolic miRNAs were underlined by significantly different structural and thermodynamic parameters. Computational targeting analysis of most mitochondrial miRNAs revealed not only nuclear but also mitochondrial-encoded targets. The functional relevance of miRNAs in mitochondria was supported by the finding of Argonaute 2 localization to mitochondria revealed by immunoblotting and confocal microscopy, and further validated by the co-immunoprecipitation of the mitochondrial transcript COX3. This study provides the first comprehensive view of the localization of RNA interference components to the mitochondria. Our data outline the molecular bases for a novel layer of crosstalk between nucleus and mitochondria through a specific subset of human miRNAs that we termed 'mitomiRs'.

Show MeSH
Related in: MedlinePlus