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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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Ontology enrichment analysis for target genes of hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638.The ExParser algorithm was used to compile datasets of genes whose expression patterns were comparable and statistically correlated to the expression patterns of the four mitomiRs. The datasets were uploaded into MetaCore™ and analyzed in respect to the Gene Ontology Process. Ten most significantly enriched processes for the genes targeted by hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638 were scored and ranked in respect to the obtained p-values. Bars represent significance as −log(p-value) for hypergeometric distribution. Ontology enrichments were all filtered to allow no more than 5% false discovery rate.
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pone-0020746-g006: Ontology enrichment analysis for target genes of hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638.The ExParser algorithm was used to compile datasets of genes whose expression patterns were comparable and statistically correlated to the expression patterns of the four mitomiRs. The datasets were uploaded into MetaCore™ and analyzed in respect to the Gene Ontology Process. Ten most significantly enriched processes for the genes targeted by hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638 were scored and ranked in respect to the obtained p-values. Bars represent significance as −log(p-value) for hypergeometric distribution. Ontology enrichments were all filtered to allow no more than 5% false discovery rate.

Mentions: We then questioned the functional relevance of those mitomiRs. To this end, we used the ExParser algorithm with the publicly available datasets to retrieve the mRNA genes experimentally classified as targets of miRNAs and/or as co-regulated in their expression with mitomiRs [36]. While lack of available experimental data precluded systematic questioning, we were able to analyze the target and/or co-regulated mRNAs for hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638 (Table S5). For each mitomiR, the compiled mRNAs were then assessed for their biological significance using a systems biology pathway analysis tool [41]. We found that all four mitomiRs were significantly involved in mitochondrial homeostasis, e.g hsa-mir-494 and hsa-mir-513 are both involved in ATP synthesis coupled electron transport (Figure 6). One common feature of their involvement pointed out their role in translation initiation and in cell cycle (Figure S4). In particular, the most significant result of hsa-mir-494 is in mitochondrial translation (p-value = 3.5×10−7) (Figure S4).


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)

Ontology enrichment analysis for target genes of hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638.The ExParser algorithm was used to compile datasets of genes whose expression patterns were comparable and statistically correlated to the expression patterns of the four mitomiRs. The datasets were uploaded into MetaCore™ and analyzed in respect to the Gene Ontology Process. Ten most significantly enriched processes for the genes targeted by hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638 were scored and ranked in respect to the obtained p-values. Bars represent significance as −log(p-value) for hypergeometric distribution. Ontology enrichments were all filtered to allow no more than 5% false discovery rate.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020746-g006: Ontology enrichment analysis for target genes of hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638.The ExParser algorithm was used to compile datasets of genes whose expression patterns were comparable and statistically correlated to the expression patterns of the four mitomiRs. The datasets were uploaded into MetaCore™ and analyzed in respect to the Gene Ontology Process. Ten most significantly enriched processes for the genes targeted by hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638 were scored and ranked in respect to the obtained p-values. Bars represent significance as −log(p-value) for hypergeometric distribution. Ontology enrichments were all filtered to allow no more than 5% false discovery rate.
Mentions: We then questioned the functional relevance of those mitomiRs. To this end, we used the ExParser algorithm with the publicly available datasets to retrieve the mRNA genes experimentally classified as targets of miRNAs and/or as co-regulated in their expression with mitomiRs [36]. While lack of available experimental data precluded systematic questioning, we were able to analyze the target and/or co-regulated mRNAs for hsa-miR-328, hsa-miR-494, hsa-miR-513 and hsa-miR-638 (Table S5). For each mitomiR, the compiled mRNAs were then assessed for their biological significance using a systems biology pathway analysis tool [41]. We found that all four mitomiRs were significantly involved in mitochondrial homeostasis, e.g hsa-mir-494 and hsa-mir-513 are both involved in ATP synthesis coupled electron transport (Figure 6). One common feature of their involvement pointed out their role in translation initiation and in cell cycle (Figure S4). In particular, the most significant result of hsa-mir-494 is in mitochondrial translation (p-value = 3.5×10−7) (Figure S4).

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