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Loss of Hilnc prevents diet-induced hepatic steatosis through binding of IGF2BP2

Nature Metabolism volume 3, pages 1569–1584 (2021)Cite this article

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Abstract

The Hedgehog (Hh) signalling pathway plays a critical role in regulating liver lipid metabolism and related diseases. However, the underlying mechanisms are poorly understood. Here, we show that the Hh signalling pathway induces a previously undefined long non-coding RNA (Hilnc, Hedgehog signalling-induced long non-coding RNA), which controls hepatic lipid metabolism. Mutation of the Gli-binding sites in the Hilnc promoter region (HilncBM/BM) decreases the expression of Hilnc in vitro and in vivo. HilncBM/BM and Hilnc-knockout mice are resistant to diet-induced obesity and hepatic steatosis through attenuation of the peroxisome proliferator-activated receptor signalling pathway, as Hilnc directly interacts with IGF2BP2 to enhance Pparγ mRNA stability. Furthermore, we identify a potential functional human homologue of Hilnc, h-Hilnc, which has a similar function in regulating cellular lipid metabolism. These findings uncover a critical role of the Hh-Hilnc–IGF2BP2 signalling axis in lipid metabolism and suggest a potential therapeutic target for the treatment of diet-induced hepatic steatosis.

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Fig. 1: Identification of GM16364 as a lncRNA (Hilnc) that is directly induced by Hedgehog signalling.
Fig. 2: Gli1 directly regulates the expression of Hilnc in vivo, and HilncBM/BM mice are resistant to diet-induced obesity.
Fig. 3: HilncBM/BM mice are resistant to diet-induced obesity and fatty liver.
Fig. 4: Lack of Hilnc decreases lipid accumulation in primary hepatocytes and prevents diet-induced hepatic steatosis.
Fig. 5: Overexpression of Hilnc in the liver of Hilnc−/− mice results in increased lipid accumulation.
Fig. 6: Hilnc modulates the PPAR signalling pathway in the liver.
Fig. 7: Hilnc directly binds to IGF2BP2 and functions through IGF2BP2.
Fig. 8: Identification of the potential functional human homologue of Hilnc.

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Data availability

RNA-seq data can be viewed in NODE (https://www.biosino.org/node/) under accession OEP001927. Biological pathways (KEGG) were analysed using DAVID (v6.8). Source data are provided with this paper. Other data that support the findings of this study are available from the corresponding author upon reasonable request.

References

  1. Rubin, L. L. & de Sauvage, F. J. Targeting the Hedgehog pathway in cancer. Nat. Rev. Drug Discov. 5, 1026–1033 (2006).

    Article  CAS  PubMed  Google Scholar 

  2. Ingham, P. W. & McMahon, A. P. Hedgehog signaling in animal development: paradigms and principles. Genes Dev. 15, 3059–3087 (2001).

    Article  CAS  PubMed  Google Scholar 

  3. Kinzler, K. W. & Vogelstein, B. The GLI gene encodes a nuclear protein which binds specific sequences in the human genome. 10, 634–642 (1990).

  4. Hallikas, O. et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, 47–59 (2006).

    Article  CAS  PubMed  Google Scholar 

  5. Pospisilik, J. A. et al. Drosophila genome-wide obesity screen reveals hedgehog as a determinant of brown versus white adipose cell fate. Cell 140, 148–160 (2010).

    Article  CAS  PubMed  Google Scholar 

  6. Suh, J. M. et al. Hedgehog signaling plays a conserved role in inhibiting fat formation. Cell Metab. 3, 25–34 (2006).

    Article  CAS  PubMed  Google Scholar 

  7. Claussnitzer, M. et al. FTO obesity variant circuitry and adipocyte browning in humans. N. Engl. J. Med. 373, 895–907 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Teperino, R. et al. Hedgehog partial agonism drives Warburg-like metabolism in muscle and brown fat. Cell 151, 414–426 (2012).

    Article  CAS  PubMed  Google Scholar 

  9. El-Agroudy, N. N., El-Naga, R. N., El-Razeq, R. A. & El-Demerdash, E. Forskolin, a hedgehog signalling inhibitor, attenuates carbon tetrachloride-induced liver fibrosis in rats. Br. J. Pharmacol. 173, 3248–3260 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Guillen-Sacoto, M. J. et al. Human germline hedgehog pathway mutations predispose to fatty liver. J. Hepatol. 67, 809–817 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Gao, L., Zhang, Z., Zhang, P., Yu, M. & Yang, T. Role of canonical Hedgehog signaling pathway in liver. Int. J. Biol. Sci. 14, 1636–1644 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Marbach-Breitruck, E. et al. Tick-tock Hedgehog-mutual crosstalk with liver circadian clock promotes liver steatosis. J. Hepatol. 70, 1192–1202 (2019).

    Article  PubMed  Google Scholar 

  13. Guy, C. D. et al. Hedgehog pathway activation parallels histologic severity of injury and fibrosis in human non-alcoholic fatty liver disease. Hepatology 55, 1711–1721 (2012).

    Article  CAS  PubMed  Google Scholar 

  14. Swiderska-Syn, M. et al. Hedgehog pathway and pediatric non-alcoholic fatty liver disease. Hepatology 57, 1814–1825 (2013).

    Article  CAS  PubMed  Google Scholar 

  15. Kwon, H. et al. Inhibition of Hedgehog signaling ameliorates hepatic inflammation in mice with non-alcoholic fatty liver disease. Hepatology 63, 1155–1169 (2016).

    Article  CAS  PubMed  Google Scholar 

  16. Choi, S. S., Omenetti, A., Syn, W. K. & Diehl, A. M. The role of Hedgehog signaling in fibrogenic liver repair. Int. J. Biochem. Cell Biol. 43, 238–244 (2011).

    Article  CAS  PubMed  Google Scholar 

  17. Matz-Soja, M. et al. Hedgehog signaling is a potent regulator of liver lipid metabolism and reveals a GLI-code associated with steatosis. Elife 5, e13308 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  18. Vokes, S. A., Ji, H., Wong, W. H. & McMahon, A. P. A genome-scale analysis of the cis-regulatory circuitry underlying sonic Hedgehog-mediated patterning of the mammalian limb. Genes Dev. 22, 2651–2663 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Vokes, S. A. et al. Genomic characterization of Gli-activator targets in sonic Hedgehog-mediated neural patterning. Development 134, 1977–1989 (2007).

    Article  CAS  PubMed  Google Scholar 

  20. Lee, E. Y. et al. Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis. Proc. Natl Acad. Sci. USA 107, 9736–9741 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Morris, K. V. & Mattick, J. S. The rise of regulatory RNA. Nat. Rev. Genet. 15, 423–437 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Huarte, M. The emerging role of lncRNAs in cancer. Nat. Med. 21, 1253–1261 (2015).

    Article  CAS  PubMed  Google Scholar 

  23. Prasanth, K. V. & Spector, D. L. Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum. Genes Dev. 21, 11–42 (2007).

    Article  CAS  PubMed  Google Scholar 

  24. Lee, J. T. Epigenetic regulation by long noncoding RNAs. Science 338, 1435–1439 (2012).

    Article  CAS  PubMed  Google Scholar 

  25. Geisler, S. & Coller, J. RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat. Rev. Mol. Cell Biol. 14, 699–712 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Quinn, J. J. & Chang, H. Y. Unique features of long non-coding RNA biogenesis and function. Nat. Rev. Genet. 17, 47–62 (2016).

    Article  CAS  PubMed  Google Scholar 

  27. Mercer, T. R., Dinger, M. E. & Mattick, J. S. Long non-coding RNAs: insights into functions. Nat. Rev. Genet. 10, 155–159 (2009).

    Article  CAS  PubMed  Google Scholar 

  28. Ponting, C. P., Oliver, P. L. & Reik, W. Evolution and functions of long non-coding RNAs. Cell 136, 629–641 (2009).

    Article  CAS  PubMed  Google Scholar 

  29. Rinn, J. L. & Chang, H. Y. Genome regulation by long non-coding RNAs. Annu. Rev. Biochem. 81, 145–166 (2012).

    Article  CAS  PubMed  Google Scholar 

  30. Chen, L. L. Linking long non-coding RNA localization and function. Trends Biochem. Sci. 41, 761–772 (2016).

    Article  CAS  PubMed  Google Scholar 

  31. Chan, L. H. et al. Hedgehog signaling induces osteosarcoma development through Yap1 and H19 overexpression. Oncogene 33, 4857–4866 (2014).

    Article  CAS  PubMed  Google Scholar 

  32. Xing, Z. et al. lncRNA directs cooperative epigenetic regulation downstream of chemokine signals. Cell 159, 1110–1125 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Zhou, M. et al. LncRNA-Hh strengthen cancer stem cells generation in twist-positive breast cancer via activation of Hedgehog signaling pathway. Stem Cells 34, 55–66 (2016).

    Article  CAS  PubMed  Google Scholar 

  34. Del Rosario, B. C. et al. Genetic intersection of Tsix and Hedgehog signaling during the initiation of X-chromosome inactivation. Dev. Cell 43, 359–371 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Wu, J. et al. The long non-coding RNA lncHDAC2 drives the self-renewal of liver cancer stem cells via activation of Hedgehog signaling. J. Hepatol. 70, 918–929 (2019).

    Article  CAS  PubMed  Google Scholar 

  36. Lin, B. J. et al. LncRNA-XIST promotes dermal papilla induced hair follicle regeneration by targeting miR-424 to activate hedgehog signaling. Cell. Signal. 72, 109623 (2020).

    Article  CAS  PubMed  Google Scholar 

  37. Zhou, H. et al. LncRNA-cCSC1 modulates cancer stem cell properties in colorectal cancer via activation of the Hedgehog signaling pathway. J. Cell. Biochem. 121, 2510–2524 (2020).

    Article  CAS  PubMed  Google Scholar 

  38. Lauth, M., Bergström, Å., Shimokawa, T. & Toftgård, R. Inhibition of GLI-mediated transcription and tumor cell growth by small-molecule antagonists. Proc. Natl Acad. Sci. USA 104, 8455–8460 (2007).

    Article  PubMed Central  Google Scholar 

  39. Ran, F. A. et al. Genome engineering using the CRISPR–Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Yao, Q., Liu, J., Xiao, L. & Wang, N. Sonic Hedgehog signaling instigates high-fat diet-induced insulin resistance by targeting PPARγ stability. J. Biol. Chem. 294, 3284–3293 (2019).

    Article  CAS  PubMed  Google Scholar 

  41. Venteclef, N., Jakobsson, T., Steffensen, K. R. & Treuter, E. Metabolic nuclear receptor signaling and the inflammatory acute-phase response. Trends Endocrinol. Metab. 22, 333–343 (2011).

    Article  CAS  PubMed  Google Scholar 

  42. Semple, R. K., Chatterjee, V. K. & O’Rahilly, S. PPARγ and human metabolic disease. J. Clin. Invest. 116, 581–589 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Vidal-Puig, A. et al. Regulation of PPARγ gene expression by nutrition and obesity in rodents. J. Clin. Invest. 97, 2553–2561 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Matsusue, K. et al. Liver-specific disruption of PPARγ in leptin-deficient mice improves fatty liver but aggravates diabetic phenotypes. J. Clin. Invest. 111, 737–747 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Lee, Y. J. et al. Nuclear receptor PPARγ-regulated monoacylglycerol O-acyltransferase 1 (MGAT1) expression is responsible for the lipid accumulation in diet-induced hepatic steatosis. Proc. Natl Acad. Sci. USA 109, 13656–13661 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129–141 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Regue, L., Minichiello, L., Avruch, J. & Dai, N. Liver-specific deletion of IGF2 mRNA binding protein-2/IMP2 reduces hepatic fatty acid oxidation and increases hepatic triglyceride accumulation. J. Biol. Chem. 294, 11944–11951 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Fornes, O. et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 48, D87–D92 (2020).

    CAS  PubMed  Google Scholar 

  49. Li, Z. et al. An HMGA2–IGF2BP2 axis regulates myoblast proliferation and myogenesis. Dev. Cell 23, 1176–1188 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Christiansen, J., Kolte, A. M., Hansen, T. & Nielsen, F. C. IGF2 mRNA-binding protein 2: biological function and putative role in type 2 diabetes. J. Mol. Endocrinol. 43, 187–195 (2009).

    Article  CAS  PubMed  Google Scholar 

  51. Dai, N. et al. IGF2BP2/IMP2-deficient mice resist obesity through enhanced translation of Ucp1 mRNA and other mRNAs encoding mitochondrial proteins. Cell Metab. 21, 609–621 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Tybl, E. et al. Overexpression of the IGF2-mRNA-binding protein p62 in transgenic mice induces a steatotic phenotype. J. Hepatol. 54, 994–1001 (2011).

    Article  CAS  PubMed  Google Scholar 

  53. Schmidt-Heck, W. et al. Fuzzy modeling reveals a dynamic self-sustaining network of the GLI transcription factors controlling important metabolic regulators in adult mouse hepatocytes. Mol. Biosyst. 11, 2190–2197 (2015).

    Article  CAS  PubMed  Google Scholar 

  54. Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26–46 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Jiang, R. et al. Transcriptome profiling of lncRNA related to fat tissues of Qinchuan cattle. Gene 742, 144587 (2020).

    Article  CAS  PubMed  Google Scholar 

  56. Tian, K. et al. DNA and RNA editing without sequence limitation using the flap endonuclease 1 guided by hairpin DNA probes. Nucleic Acids Res. 48, e117 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Kong, L. et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35, W345–W349 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  59. Wang, L. et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 41, e74 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Yang, H., Wang, H. & Jaenisch, R. Generating genetically modified mice using CRISPR–Cas-mediated genome engineering. Nat. Protoc. 9, 1956–1968 (2014).

    Article  CAS  PubMed  Google Scholar 

  61. Li, W. C., Ralphs, K. L. & Tosh, D. Isolation and culture of adult mouse hepatocytes. Methods Mol. Biol. 633, 185–196 (2010).

    Article  CAS  PubMed  Google Scholar 

  62. Kawaguchi, T. et al. SWI/SNF chromatin-remodeling complexes function in non-coding RNA-dependent assembly of nuclear bodies. Proc. Natl Acad. Sci. USA 112, 4304–4309 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Harada, N. et al. Hepatic de novo lipogenesis is present in liver-specific ACC1-deficient mice. Mol. Cell Biol. 27, 1881–1888 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank the animal facility for animal husbandry, and technical supports from Core Facility for Cell Biology and the Genome Tagging Project Center, at CEMC. We acknowledge W. Yang for the providing reagents and helpful comments. This study was supported by grants from the National Key Research and Development Program of China (2020YFA0509000 and 2017YFA0503600 to Y.Z. and 2017YFA0505500 to D.G.), the National Natural Science Foundation of China (32130025 and 31630047 to Y.Z., 81772723 and 81830054 to D.G., 81874201 to M.B.L. and 31801184 to J.Y.P.), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16020905 to D.G.), the Basic Frontier Science Research Program of the Chinese Academy of Sciences (ZDBS-LY-SM015 to D.G.), the CAS-VPST Silk Road Science Fund 2019 (GJHZ201968 to D.G.) and the Science and Technology Commission of Shanghai Municipality (20Y11908300 to M.B.L.).

Author information

Author notes

  1. These authors contributed equally: Yiao Jiang, Jiayin Peng.

Authors and Affiliations

  1. The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China

    Yiao Jiang, Jiayin Peng, Jiawen Song, Juan He, Jia Wang, Liya Ma, Yuang Wang, Dong Gao & Yun Zhao

  2. School of Life Science and Technology, ShanghaiTech University, Shanghai, China

    Man Jiang & Yun Zhao

  3. Department of General Surgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai, P. R. China

    Moubin Lin

  4. Shanghai Key Laboratory for Molecular Imaging, Collaborative Research Center, Shanghai University of Medicine and Health Science, Shanghai, P. R. China

    Hailong Wu

  5. Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA

    Zhao Zhang

  6. Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA

    Zhao Zhang

  7. Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shangha, China

    Dong Gao

  8. Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China

    Dong Gao

  9. School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China

    Yun Zhao

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Contributions

Y.Z. conceived and designed the experimental approach. Y.A.J. performed most of the experiments. J.Y.P. contributed to the mouse experiments and statistical analysis. J.W.S., M.J., J.W., L.Y.M., Y.A.W. and J.H. helped the experiments and provided technical support. M.B.L., Z.Z., H.L.W. and D.G. helped to design experiments and provided useful discussion. Y.A.J. and Y.Z. wrote the manuscript.

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Correspondence to Yun Zhao.

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Extended data

Extended Data Fig. 1 Characterization of Hilnc.

a, One TSS was identified with 5’ cap adapter using 5’ RACE primer, and two transcriptional ending sites were identified with 3’ poly (A) adapter using 3’ RACE primer in RACE assay. The upper part showed the two isoforms of Hilnc. b, Relative expression of two isoforms of Hilnc in NIH-3T3 cells was measured by qPCR (n = 3 biologically independent samples). c, A description of Hilnc’s locus. d, The full sequence of two isoforms of Hilnc. e, Hilnc accumulated in the cytoplasm. Total NIH-3T3 cell lysate was separated into cytoplasmic and nuclear fractions, and analyzed by western blot and qPCR (n = 3 biologically independent samples). For western blot, β-Tubulin was employed as a control for cytoplasm and Histone H3 for nucleolus. For qPCR, Gapdh was employed as a control for cytoplasm and U6 for nucleolus. f, A luciferase reporter driven by the WT Hilnc promoter was transfected with different concentrations of GLI1 (n = 3 biologically independent samples). The P value was calculated by two-tailed unpaired t-test. Data are means ± SEM.

Source data

Extended Data Fig. 2 The expression of Hilnc, Gli1, Ptch1 in the different organs of mice fed a NCD or HFD.

a,b,c, Total RNA was extracted from the muscle (a), WAT (b) or BAT (c) of 22-week-old male mice fed a NCD or HFD for 16 weeks (n = 3 biologically independent samples). Relative expression levels were normalized to the 18 s RNA level. The P value was calculated by two-tailed unpaired t-test. Data are means ± SEM.

Extended Data Fig. 3 Generation and phenotype of Hilnc-/- and HilncBM/BM mice.

a, PCR analysis of 4-week-old mice revealed the presence of Hilnc-/- and HilncBM/BM mice as expected. b,c,d,e, Relative expression of Hilnc in the MEF (b), muscle (c), WAT (d) or BAT (e) of Hilnc-/- and HilncBM/BM mice (n = 3 biologically independent samples). f,g, Representative images (f) and body weights (g, n = 4 biologically independent samples) were monitored in 8-week-old WT, Hilnc-/- or HilncBM/BM male mice. h, Glucose tolerance tests of 10-week-old WT and HilncBM/BM male mice fed a NCD (n = 4 biologically independent animals). i, Insulin tolerance tests of 10-week-old WT and HilncBM/BM male mice fed a NCD (n = 4 biologically independent animals). j, Growth curves of WT and Hilnc-/- mice on a NCD and HFD, respectively (n = 5 biologically independent animals). The P values were 0.0044, 0.0001, 0.0050, 0.0052, 0.0082, 0.4215, 0.0067, 0.0042, 0.0051 and 0.0050 (left to right). k, Representative images of 22-week-old WT and Hilnc-/- male mice fed a HFD for 16 weeks. l, Representative images of abdominal WAT (upper) and liver (lower) from 22-week-old WT or Hilnc-/- male mice fed a HFD for 16 weeks. m, H&E and oil Red O staining of liver sections from WT and Hilnc-/- mice fed a HFD; scale bar, 50 μm. The P value was calculated by two-tailed unpaired t-test. Data are means ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001.

Extended Data Fig. 4 Food intake, fecal fat, physical activity counts, respiratory quotient and energy expenditure in WT and HilncBM/BM mice.

a,b,c, Food intake (a), physical activity per 24 hours in X-Y direction (b), respiratory quotient (RER) (c) of male WT and HilncBM/BM mice at 14 weeks of age on a NCD (left, n = 4 biologically independent animals) and HFD (right, n = 6 biologically independent animals). d,e, Fecal weight (d), and percent fecal weight as TG (e) on a HFD (n = 6 biologically independent animals). f, Energy expenditure (EE) of WT and HilncBM/BM mice at 14 weeks of age on a NCD (left, n = 4 biologically independent animals) and HFD (right, n = 6 biologically independent animals). The P value was calculated by two-tailed unpaired t-test. Data are means ± SEM.

Extended Data Fig. 5 The overall metabolic characteristics of mice with liver-specific Hilnc manipulation.

a,b,c, Body weight (a), energy expenditure (b), and glucose tolerance test (c) of Hilnc knockdown mice and WT maintained on HFD for 10 weeks (n = 5 biologically independent animals). d,e,f, Body weight (d), energy expenditure (e), and glucose tolerance test (f) of Hilnc-/- (O/E-Hilnc) mice and Hilnc-/- (AAV8-Control) mice maintained on HFD for 10 weeks (n = 5 biologically independent animals). The data represent the mean ± SEM. Two-tailed unpaired t test was used to compare the difference between groups.

Extended Data Fig. 6 The gene expression level in the livers of WT and HilncBM/BM mice fed a NCD or HFD.

a, Volcano plot showing the changed genes in the livers of 22-week-old HilncBM/BM mice fed a NCD for 16 weeks compared with WT livers. b, KEGG pathway enrichment analysis of transcripts differentially expressed between livers isolated from WT and HilncBM/BM mice fed a NCD. c, Upregulated KEGG pathway enrichment analysis of transcripts differentially expressed between livers isolated from WT and HilncBM/BM mice fed a HFD. d, Heat map showing the changed genes that were enriched in different upregulated KEGG pathways. The heatmap is draw based on normalized expression levels. e, Western bolt showed the protein level of PPARγ in the livers of WT and HilncBM/BM mice fed a NCD.

Source data

Extended Data Fig. 7 Hilnc has no cis activity.

a, Locus of Hilnc (red) and its nearby coding genes (blue), Traf3ip2 and Fyn, on chromosome 10. b, The mRNA (left, n = 3 biologically independent samples) and protein level (right, n = 2 biologically independent samples) of Traf3ip2 and Fyn in the livers of WT and Hilnc-/- mice. c, The mRNA (left, n = 3 biologically independent samples) and protein levels (right, n = 2 biologically independent samples) of Traf3ip2 and Fyn in the livers of WT and HilncBM/BM mice. The P value was calculated by two-tailed unpaired t-test. Data are means ± SEM.

Source data

Extended Data Fig. 8 Identification of potential human homolog of Hilnc.

a, The locus of Hilnc on chromosome 10 in mouse genome. b, The relative locus of Hilnc in human genome. c, One TSS was identified using 5’ RACE primer, and one transcriptional ending sites was identified using 3’ RACE primer in RACE assay. d,e, The locus of ENST00000417084.1 (h-Hilnc) in human genome and the relative locus of h-Hilnc in mouse genome. f, The whole sequence of h-Hilnc. g, The conservation information of h-Hilnc in NONCODE.

Supplementary information

Supplementary Information

Supplementary Tables 1 and 5–7

Reporting Summary

Supplementary Table 2

The DEGs in the livers of WT and HilncBM/BM mice fed a HFD.

Supplementary Table 3

The sequencing data of genes and lncRNAs in the immunoprecipitation samples.

Supplementary Table 4

The differentially expressed lncRNAs in the LO2 cells treated with and without OA.

Source data

Source Data Fig. 6

Unprocessed western blots.

Source Data Fig. 7

Unprocessed western blots and gels.

Source Data Extended Data Fig. 1

Unprocessed western blots.

Source Data Extended Data Fig. 6

Unprocessed western blots.

Source Data Extended Data Fig. 7

Unprocessed western blots.

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Jiang, Y., Peng, J., Song, J. et al. Loss of Hilnc prevents diet-induced hepatic steatosis through binding of IGF2BP2. Nat Metab 3, 1569–1584 (2021). https://doi.org/10.1038/s42255-021-00488-3

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