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MDRL lncRNA regulates the processing of miR-484 primary transcript by targeting miR-361.

Wang K, Sun T, Li N, Wang Y, Wang JX, Zhou LY, Long B, Liu CY, Liu F, Li PF - PLoS Genet. (2014)

Bottom Line: The results showed that miR-361 that predominantly located in nucleus can directly bind to primary transcript of miR-484 (pri-miR-484) and prevent its processing by Drosha into pre-miR-484. miR-361 is able to regulate mitochondrial fission and apoptosis by regulating miR-484 levels.Our present study reveals a novel regulating model of mitochondrial fission program which is composed of MDRL, miR-361 and miR-484.Our work not only expands the function of the lncRNA pathway in gene regulation but also establishes a new mechanism for controlling miRNA expression.

View Article: PubMed Central - PubMed

Affiliation: Division of Cardiovascular Research, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.

ABSTRACT
Long noncoding RNAs (lncRNAs) are emerging as new players in gene regulation, but whether lncRNAs operate in the processing of miRNA primary transcript is unclear. Also, whether lncRNAs are involved in the regulation of the mitochondrial network remains to be elucidated. Here, we report that a long noncoding RNA, named mitochondrial dynamic related lncRNA (MDRL), affects the processing of miR-484 primary transcript in nucleus and regulates the mitochondrial network by targeting miR-361 and miR-484. The results showed that miR-361 that predominantly located in nucleus can directly bind to primary transcript of miR-484 (pri-miR-484) and prevent its processing by Drosha into pre-miR-484. miR-361 is able to regulate mitochondrial fission and apoptosis by regulating miR-484 levels. In exploring the underlying molecular mechanism by which miR-361 is regulated, we identified MDRL and demonstrated that it could directly bind to miR-361 and downregulate its expression levels, which promotes the processing of pri-miR-484. MDRL inhibits mitochondrial fission and apoptosis by downregulating miR-361, which in turn relieves inhibition of miR-484 processing by miR-361. Our present study reveals a novel regulating model of mitochondrial fission program which is composed of MDRL, miR-361 and miR-484. Our work not only expands the function of the lncRNA pathway in gene regulation but also establishes a new mechanism for controlling miRNA expression.

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miR-361 in the nucleus is able to regulate mature miR-484 levels.A. Microarray results depicting the log-log scatter plot of intensity of miRNA expression in nuclei from control versus A/R treatment. The neonatal mouse cardiomyocytes were untreated (control) or exposed to A/R. The nuclei were purified and nuclear miRNAs were detected by microarray. The red dots and the green dots indicate 2 fold up- or down-regulated genes, respectively. B. Upregulated nuclear miRNAs upon A/R treatment. C. Knockdown of miR-361 elevates the levels of miR-484. Cardiomyocytes were transfected with indicated miRNA antagomir (anta-miRNA) or the antagomir control (anta-control). 48 h after transfection, miR-484 levels were analyzed by qRT-PCR. *p<0.05 vs anta-control. D. miR-361 predominantly localizes in the cell nucleus and miR-484 predominantly localizes in the cytoplasm. Total RNA was extracted from cardiomyocytes nucleus and cytoplasm. miR-361 and miR-484 levels were analyzed by northern blot. E. Enforced expression of miR-361 reduces the levels of miR-484. Cardiomyocytes were infected with adenoviral miR-361 or β-gal at a moi of 80. 24 h after infection, the expression of miR-484 was analyzed by northern blot. F. miR-361 suppresses the expression of miR-484 in the animal model. miR-484 levels in the hearts of WT and miR-361 transgenic mice were analyzed by northern blot.
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pgen-1004467-g001: miR-361 in the nucleus is able to regulate mature miR-484 levels.A. Microarray results depicting the log-log scatter plot of intensity of miRNA expression in nuclei from control versus A/R treatment. The neonatal mouse cardiomyocytes were untreated (control) or exposed to A/R. The nuclei were purified and nuclear miRNAs were detected by microarray. The red dots and the green dots indicate 2 fold up- or down-regulated genes, respectively. B. Upregulated nuclear miRNAs upon A/R treatment. C. Knockdown of miR-361 elevates the levels of miR-484. Cardiomyocytes were transfected with indicated miRNA antagomir (anta-miRNA) or the antagomir control (anta-control). 48 h after transfection, miR-484 levels were analyzed by qRT-PCR. *p<0.05 vs anta-control. D. miR-361 predominantly localizes in the cell nucleus and miR-484 predominantly localizes in the cytoplasm. Total RNA was extracted from cardiomyocytes nucleus and cytoplasm. miR-361 and miR-484 levels were analyzed by northern blot. E. Enforced expression of miR-361 reduces the levels of miR-484. Cardiomyocytes were infected with adenoviral miR-361 or β-gal at a moi of 80. 24 h after infection, the expression of miR-484 was analyzed by northern blot. F. miR-361 suppresses the expression of miR-484 in the animal model. miR-484 levels in the hearts of WT and miR-361 transgenic mice were analyzed by northern blot.

Mentions: Many studies have observed that there exist mature miRNAs in the nucleus [12], [18]–[23] and recent work also reports that let-7 miRNA in the nucleus can regulate its own primary transcript through a conserved complementary site, thus creating a positive-feedback loop [11]. Our previous work has showed that transcription factor could regulate miR-484 expression [24]. To further explore other underlying mechanism responsible for miR-484 regulation under anoxia/reoxygenation (A/R) condition, we tested whether miRNA in the nucleus participates in the regulation of miR-484 expression. To understand which nuclear miRNA is involved in the apoptosis pathway of A/R, we performed a microarray to detect nuclear miRNAs in response to A/R treatment (Figure 1A, Figure 1B and Table S1) and among these miRNAs induced by A/R, only knockdown of endogenous miR-361 (Figure S1A) induced an increase in the miR-484 expression levels (Figure 1C). A further study confirmed that miR-361 was predominantly located in the nucleus, and miR-484 was predominantly located in the cytoplasm (Figure 1D). We test whether nuclear miR-361 may directly affect the expression of miR-484. The results showed that enforced expression of miR-361 could reduce mature miR-484 levels (Figure 1E). Furthermore, miR-361 transgenic mice (Figures S1B and S1C) demonstrated reduced levels of miR-484 in the animal model (Figure S1D and Figure 1F). Taken together, it appears that miR-361 is predominantly located in the nucleus and is able to regulate mature miR-484 levels in the cellular and the animal model.


MDRL lncRNA regulates the processing of miR-484 primary transcript by targeting miR-361.

Wang K, Sun T, Li N, Wang Y, Wang JX, Zhou LY, Long B, Liu CY, Liu F, Li PF - PLoS Genet. (2014)

miR-361 in the nucleus is able to regulate mature miR-484 levels.A. Microarray results depicting the log-log scatter plot of intensity of miRNA expression in nuclei from control versus A/R treatment. The neonatal mouse cardiomyocytes were untreated (control) or exposed to A/R. The nuclei were purified and nuclear miRNAs were detected by microarray. The red dots and the green dots indicate 2 fold up- or down-regulated genes, respectively. B. Upregulated nuclear miRNAs upon A/R treatment. C. Knockdown of miR-361 elevates the levels of miR-484. Cardiomyocytes were transfected with indicated miRNA antagomir (anta-miRNA) or the antagomir control (anta-control). 48 h after transfection, miR-484 levels were analyzed by qRT-PCR. *p<0.05 vs anta-control. D. miR-361 predominantly localizes in the cell nucleus and miR-484 predominantly localizes in the cytoplasm. Total RNA was extracted from cardiomyocytes nucleus and cytoplasm. miR-361 and miR-484 levels were analyzed by northern blot. E. Enforced expression of miR-361 reduces the levels of miR-484. Cardiomyocytes were infected with adenoviral miR-361 or β-gal at a moi of 80. 24 h after infection, the expression of miR-484 was analyzed by northern blot. F. miR-361 suppresses the expression of miR-484 in the animal model. miR-484 levels in the hearts of WT and miR-361 transgenic mice were analyzed by northern blot.
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Related In: Results  -  Collection

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pgen-1004467-g001: miR-361 in the nucleus is able to regulate mature miR-484 levels.A. Microarray results depicting the log-log scatter plot of intensity of miRNA expression in nuclei from control versus A/R treatment. The neonatal mouse cardiomyocytes were untreated (control) or exposed to A/R. The nuclei were purified and nuclear miRNAs were detected by microarray. The red dots and the green dots indicate 2 fold up- or down-regulated genes, respectively. B. Upregulated nuclear miRNAs upon A/R treatment. C. Knockdown of miR-361 elevates the levels of miR-484. Cardiomyocytes were transfected with indicated miRNA antagomir (anta-miRNA) or the antagomir control (anta-control). 48 h after transfection, miR-484 levels were analyzed by qRT-PCR. *p<0.05 vs anta-control. D. miR-361 predominantly localizes in the cell nucleus and miR-484 predominantly localizes in the cytoplasm. Total RNA was extracted from cardiomyocytes nucleus and cytoplasm. miR-361 and miR-484 levels were analyzed by northern blot. E. Enforced expression of miR-361 reduces the levels of miR-484. Cardiomyocytes were infected with adenoviral miR-361 or β-gal at a moi of 80. 24 h after infection, the expression of miR-484 was analyzed by northern blot. F. miR-361 suppresses the expression of miR-484 in the animal model. miR-484 levels in the hearts of WT and miR-361 transgenic mice were analyzed by northern blot.
Mentions: Many studies have observed that there exist mature miRNAs in the nucleus [12], [18]–[23] and recent work also reports that let-7 miRNA in the nucleus can regulate its own primary transcript through a conserved complementary site, thus creating a positive-feedback loop [11]. Our previous work has showed that transcription factor could regulate miR-484 expression [24]. To further explore other underlying mechanism responsible for miR-484 regulation under anoxia/reoxygenation (A/R) condition, we tested whether miRNA in the nucleus participates in the regulation of miR-484 expression. To understand which nuclear miRNA is involved in the apoptosis pathway of A/R, we performed a microarray to detect nuclear miRNAs in response to A/R treatment (Figure 1A, Figure 1B and Table S1) and among these miRNAs induced by A/R, only knockdown of endogenous miR-361 (Figure S1A) induced an increase in the miR-484 expression levels (Figure 1C). A further study confirmed that miR-361 was predominantly located in the nucleus, and miR-484 was predominantly located in the cytoplasm (Figure 1D). We test whether nuclear miR-361 may directly affect the expression of miR-484. The results showed that enforced expression of miR-361 could reduce mature miR-484 levels (Figure 1E). Furthermore, miR-361 transgenic mice (Figures S1B and S1C) demonstrated reduced levels of miR-484 in the animal model (Figure S1D and Figure 1F). Taken together, it appears that miR-361 is predominantly located in the nucleus and is able to regulate mature miR-484 levels in the cellular and the animal model.

Bottom Line: The results showed that miR-361 that predominantly located in nucleus can directly bind to primary transcript of miR-484 (pri-miR-484) and prevent its processing by Drosha into pre-miR-484. miR-361 is able to regulate mitochondrial fission and apoptosis by regulating miR-484 levels.Our present study reveals a novel regulating model of mitochondrial fission program which is composed of MDRL, miR-361 and miR-484.Our work not only expands the function of the lncRNA pathway in gene regulation but also establishes a new mechanism for controlling miRNA expression.

View Article: PubMed Central - PubMed

Affiliation: Division of Cardiovascular Research, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.

ABSTRACT
Long noncoding RNAs (lncRNAs) are emerging as new players in gene regulation, but whether lncRNAs operate in the processing of miRNA primary transcript is unclear. Also, whether lncRNAs are involved in the regulation of the mitochondrial network remains to be elucidated. Here, we report that a long noncoding RNA, named mitochondrial dynamic related lncRNA (MDRL), affects the processing of miR-484 primary transcript in nucleus and regulates the mitochondrial network by targeting miR-361 and miR-484. The results showed that miR-361 that predominantly located in nucleus can directly bind to primary transcript of miR-484 (pri-miR-484) and prevent its processing by Drosha into pre-miR-484. miR-361 is able to regulate mitochondrial fission and apoptosis by regulating miR-484 levels. In exploring the underlying molecular mechanism by which miR-361 is regulated, we identified MDRL and demonstrated that it could directly bind to miR-361 and downregulate its expression levels, which promotes the processing of pri-miR-484. MDRL inhibits mitochondrial fission and apoptosis by downregulating miR-361, which in turn relieves inhibition of miR-484 processing by miR-361. Our present study reveals a novel regulating model of mitochondrial fission program which is composed of MDRL, miR-361 and miR-484. Our work not only expands the function of the lncRNA pathway in gene regulation but also establishes a new mechanism for controlling miRNA expression.

Show MeSH
Related in: MedlinePlus