Long noncoding RNA Tug1 regulates mitochondrial bioenergetics in diabetic nephropathy
Jianyin Long, … , Paul A. Overbeek, Farhad R. Danesh
Jianyin Long, … , Paul A. Overbeek, Farhad R. Danesh
Published October 17, 2016
Citation Information: J Clin Invest. 2016;126(11):4205-4218. https://doi.org/10.1172/JCI87927.
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Research Article Nephrology

Long noncoding RNA Tug1 regulates mitochondrial bioenergetics in diabetic nephropathy

Abstract

The regulatory roles of long noncoding RNAs (lncRNAs) in transcriptional coactivators are still largely unknown. Here, we have shown that the peroxisome proliferator–activated receptor γ (PPARγ) coactivator α (PGC-1α, encoded by Ppargc1a) is functionally regulated by the lncRNA taurine-upregulated gene 1 (Tug1). Further, we have described a role for Tug1 in the regulation of mitochondrial function in podocytes. Using a murine model of diabetic nephropathy (DN), we performed an unbiased RNA-sequencing (RNA-seq) analysis of kidney glomeruli and identified Tug1 as a differentially expressed lncRNA in the diabetic milieu. Podocyte-specific overexpression (OE) of Tug1 in diabetic mice improved the biochemical and histological features associated with DN. Unexpectedly, we found that Tug1 OE rescued the expression of PGC-1α and its transcriptional targets. Tug1 OE was also associated with improvements in mitochondrial bioenergetics in the podocytes of diabetic mice. Mechanistically, we found that the interaction between Tug1 and PGC-1α promotes the binding of PGC-1α to its own promoter. We identified a Tug1-binding element (TBE) upstream of the Ppargc1a gene and showed that Tug1 binds with the TBE to enhance Ppargc1a promoter activity. These findings indicate that a direct interaction between PGC-1α and Tug1 modulates mitochondrial bioenergetics in podocytes in the diabetic milieu.

Authors

Jianyin Long, Shawn S. Badal, Zengchun Ye, Yin Wang, Bernard A. Ayanga, Daniel L. Galvan, Nathanael H. Green, Benny H. Chang, Paul A. Overbeek, Farhad R. Danesh

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Figure 5

ChIRP-seq analysis reveals genome-wide binding sites for Tug1, including a TBE upstream of the Ppargc1a promoter.

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ChIRP-seq analysis reveals genome-wide binding sites for Tug1, including...
(A) Biotinylated Tug1 antisense DNA probes retrieved approximately 77% of total Tug1 RNA. Biotinylated LacZ antisense DNA probes were unable to retrieve either RNA. **P < 0.01, by 2-tailed Student’s t test. Data are expressed as the mean ± SEM. (B) Percentage of Tug1-binding sites localized to different regions within the genome. LTR, long-terminal repeat; LINE, long-interspersed repetitive element; SINE, short-interspersed repetitive element. (C) Purine-rich stretches, either GA repeats or A repeats, represented the top scoring motifs among Tug1-binding sites. (D) Top GO analysis categories of biological processes related to Tug1-binding sites represented as enrichment scores: –log10(P value). (E) ChIRP-seq tag density at an intergenic, putative TBE approximately 400 kb upstream of the Ppargc1a gene promoter. Data are represented as Tug1-pulldown compared with input controls. Track heights were normalized to allow for comparison between groups. Tug1-pulldown data were generated from overlapping peak data from biological replicates of Tug1-odd pulldown and Tug1-even pulldown samples compared with input. Zoom inset highlights the peak height, and the location of MACS verified the peak. Aligned reads were used for peak calling of the ChIRP regions using MACS, version 1.4.0. gDNA, genomic DNA. Statistically significant ChIRP-enriched regions (peaks) were identified by comparison with input, using a P-value threshold of 10–5. Cell culture experiments were repeated at least 3 times. GO analysis was applied to peaks to determine the roles played in certain biological pathways or GO terms.