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Glis1 facilitates induction of pluripotency via an epigenome–metabolome–epigenome signalling cascade

Nature Metabolism volume 2, pages 882–892 (2020)Cite this article

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An Author Correction to this article was published on 08 October 2020

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Abstract

Somatic cell reprogramming provides insight into basic principles of cell fate determination, which remain poorly understood. Here we show that the transcription factor Glis1 induces multi-level epigenetic and metabolic remodelling in stem cells that facilitates the induction of pluripotency. We find that Glis1 enables reprogramming of senescent cells into pluripotent cells and improves genome stability. During early phases of reprogramming, Glis1 directly binds to and opens chromatin at glycolytic genes, whereas it closes chromatin at somatic genes to upregulate glycolysis. Subsequently, higher glycolytic flux enhances cellular acetyl-CoA and lactate levels, thereby enhancing acetylation (H3K27Ac) and lactylation (H3K18la) at so-called ‘second-wave’ and pluripotency gene loci, opening them up to facilitate cellular reprogramming. Our work highlights Glis1 as a powerful reprogramming factor, and reveals an epigenome–metabolome–epigenome signalling cascade that involves the glycolysis-driven coordination of histone acetylation and lactylation in the context of cell fate determination.

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Fig. 1: Glis1 activates glycolysis genes and suppresses the somatic cell state during somatic cell reprogramming.
Fig. 2: Glycolytic genes are downstream targets of Glis1 during somatic cell reprogramming.
Fig. 3: Glis1 switches the metabolic state during somatic cell reprogramming.
Fig. 4: Glis1 increases histone H3K27Ac and H3K18la at pluripotency loci, opening and activating pluripotent genes.

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Data availability

The data supporting the findings of this study are available from the corresponding author on reasonable request. RNA-seq and ChIP–seq data are available in the Gene Expression Omnibus database under the accession number GSE131692. ATAC–seq raw sequence data reported in this paper have been deposited in the Genome Sequence Archive49 at the Beijing Institute of Genomics (BIG) Data Center50, BIG, Chinese Academy of Sciences, under accession number CRA002469, which is publicly accessible at https://bigd.big.ac.cn/gsa. Source data for Figs. 1–4 and Extended Data Figs. 1–6 are presented within the paper. Source data are provided with this paper.

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Acknowledgements

We thank J. Chen for providing pMXs-Glis1 plasmids. We also thank all the members in X.L.’s laboratory. This work was financially supported by the National Key Research and Development Program of China (grant no. 2018YFA0107100), the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no. XDA16030505), the National Key Research and Development Program of China (grant nos. 2017YFA0106300, 2017YFA0102900, 2017YFC1001602, 2019YFA09004500, 2016YFA0100300), the National Natural Science Foundation projects of China (grant nos. U1601227, 31631163001, 31701281, 31701106, 31801168, 31900614, 31970709, 81901275), the Key Research Program of Frontier Sciences, Chinese Academy of Sciences (CAS) (grant no. QYZDB-SSW-SMC001), CAS STS Program KFJ-STS-QYZD-125, Guangzhou Health Care and Cooperative Innovation Major Project (grant no. 201704020218), Guangdong Province Science and Technology Program (grant nos. 2017B020230005, 2017A020215056, 2017B030314056, 2018A030313825, 2018GZR110103002, 2020A1515011200, 2020A1515010919, 2020A1515011410), Guangzhou Science and Technology Program (grant nos. 201707010178, 201807010067, 202002030277), a grant from Yangtse River Scholar Bonus Schemes (to X.L.) and CAS Youth Innovation Promotion Association (to K.C.).

Author information

Author notes

  1. These authors contributed equally: Linpeng Li, Keshi Chen, Tianyu Wang, Yi Wu.

Authors and Affiliations

  1. Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China

    Linpeng Li, Keshi Chen, Tianyu Wang, Yi Wu, Guangsuo Xing, Mengqi Chen, Zhihong Hao, Bochao Ma, Zihuang Liu, Hao Yuan, Zijian Liu, Qi Long, Yanshuang Zhou, Juntao Qi, Danyun Zhao, Mi Gao, Duanqing Pei, Jinfu Nie, Guangjin Pan & Xingguo Liu

  2. Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Guangzhou, China

    Linpeng Li, Keshi Chen, Tianyu Wang, Yi Wu, Guangsuo Xing, Mengqi Chen, Zhihong Hao, Bochao Ma, Zihuang Liu, Hao Yuan, Zijian Liu, Qi Long, Yanshuang Zhou, Juntao Qi, Danyun Zhao, Mi Gao, Duanqing Pei, Jinfu Nie, Guangjin Pan & Xingguo Liu

  3. Fudan University, Shanghai, China

    Cheng Zhang, Jinye Zhang & Dan Ye

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Contributions

X.L. conceived, designed and supervised the project. L.L., K.C. and Y.W. designed and performed the experiments and analysed data. G.X., B.M., M.C., Zihuang Liu, Zijian Liu and Z.H. participated in plasmids construction. Q.L., Y.Z., J.Q., M.G., H.Y. and D.Z. participated in iPSC generation and ChIP experiments. T.W., G.P. and J.N. participated in ChIP–seq, RNA-seq and ATAC–seq data analysis. D.P. gave suggestions. C.Z., J.Z. and D.Y. participated in metabolome analysis. X.L., L.L., Y.W. and K.C. wrote the manuscript.

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Correspondence to Xingguo Liu.

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The authors declare no competing interests.

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Extended data

Extended Data Fig. 1 Pluripotency identification of iPSCs derived from senescent somatic cells.

a, OG2 MEFs were infected with retroviral SKO plus Flag or Glis1. GFP+ colonies were counted on day12, day14, day16, day18, day20. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. b, OG2 MEFs were infected with retroviral SKO plus Flag or Glis1. (left): GFP colony pictures on day35 during reprogramming; (right): GFP+ colonies were counted on the indicated days during reprogramming. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. c, Bright and β-gal staining images of P2-MEFs, P7-MEFs, P8-Flag-MEFs and P8-Glis1 expressed stably MEFs (P8-Glis1-MEFs) (a senescent cell was circled in red in MEFs). Scale bar: 100 μm. One replicate (n = 1, each group) was used for bright and β-gal staining images analysis. n = 3 independent experiments were repeated with similar results (a–b). d, β-gal positive cells counting for P2-MEFs, P7- MEFs (left); P8-Flag-MEFs, P8-Glis1-MEFs (right). Data are presented as the mean ± S.D. (P2-MEFs, n=52; P7- MEFs, n=58; P8-Flag-MEFs, n=58; P8-Glis1-MEFs, n=75 fields, each group).Group differences are analyzed by the two-tailed Student’s t test. e, Cell proliferation capacity analysis of P2-MEFs, P7-MEFs (left); P8-Flag-MEFs, P8-Glis1-MEFs (right) by Edu. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. f, RT-qPCR analysis for detecting the expression of p16, p21 and p53 in P8-Flag-MEFs or P8-Glis1-MEFs. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. g, Western blot analysis of P16, P21 and P53 upon Glis1 overexpression in P8-Flag-MEFs or P8-Glis1-MEFs (n = 1 independent experiments). h, Oct4-GFP images and immunofluorescence staining for the indicated pluripotency markers (red) for P7-iPSCs and P8-iPSCs clones derived from OG2 MEFs (n = 6 clonies for each group). Scale bar: 50 μm (left); RT-qPCR showing endogenous expression of indicated pluripotency genes in MEFs, mouse embryonic stem cells (R1) and P7-iPSCs and P8-iPSCs clones (right).

Source data

Extended Data Fig. 2 ChIP-Seq analysis of Glis1 during somatic cell reprogramming.

a, DNA integrity assessment of P10 control-iPSCs and Glis1-iPSCs by comet assay. The experiment were performed twice, and the data are represented as mean ± S.E.M, (Ctrl, n=134; Glis1, n=187 cell nucleus). Group differences are analyzed by the two-tailed Student’s t test. b, RT-qPCR analysis for detecting the expression of endogenous Glis1 during SKO-mediated reprogramming. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. c, RT-qPCR analysis for detecting the Glis1 knockdown efficiency in MEFs relative to shLuc control. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. d, OG2 MEFs were infected with retroviral SKO and shRNAs against Luciferase (shLuc) or Glis1 (shGlis1). GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. e, Schematic maps of Glis1 truncations used in this study; numbers are for amino acids. f, OG2 MEFs were infected with retroviral SKO plus Glis1 wild-type or deletion mutants. GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. g, RT-qPCR analysis for detecting the Glis1 knockdown efficiency in MEFs relative to shLuc control in DOX-inducible knockdown system. Data are presented as the mean ± S.D. (n =4, each group).Group differences are analyzed by the two-tailed Student’s t test. h, OG2 MEFs were infected with retroviral SKO and DOX-inducible knockdown of Glis1. DOX was added immediately after infection until the indicated day or added from indicated day until day 20. The reprogramming efficiencies were compared with DOX-free control. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. i, OG2 MEFs were infected with retroviral SKO and DOX-inducible Glis1. DOX was added immediately after infection until the indicated day or added from indicated day until day 20. The reprogramming efficiencies were compared with DOX-free control. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. j, The Glis1-N-HA-tag enhanced iPSCs generation equally well as non-tag Glis1. GFP+ colonies were determined on day 20. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. k, GO term analysis of Glis1 peak position to nearest genes by ChIP-seq. 1 replicate was used for Go term analysis in Glis1 ChIP-seq assay. n = 2 independent experiments were repeated with similar results (a–c). l, Genome view of Glis1 binding at indicated gene loci by ChIP-seq. Scale bar, 5 kb. n = 2 independent experiments were repeated with similar results (k–j). Pie chart indicating the number of genes upregulated, downregulated or unchanged upon Glis1 overexpression on day 8. 1 replicate was used for RNA-seq analysis. n = 2 independent experiments were repeated with similar results.

Source data

Extended Data Fig. 3 Glis1 suppressed somatic state genes during somatic cell reprogramming.

a, The binding of Glis1 on glycolytic process gene loci was determined by ChIP–qPCR. TF-NC represents negative control. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. b, Time courses of qPCR analyses of somatic state gene expression levels by SKO plus Flag and SKO plus Glis1. Data are presented as the mean ± S.D. (Setbp1, Col11a1 n=3; other genes, n=4 each group).Group differences are analyzed by the two-tailed Student’s t test. c, RT-qPCR analysis for detecting the glycolysis genes knockdown efficiency in MEFs.

Source data

Extended Data Fig. 4 Glis1 did not suppress OCR during somatic cell reprogramming.

a, Mitochondrial stress test using Seahorse XF24 analyzer on day 8. SKO plus Flag as a control compared to SKO plus Glis1. Flag as the control to all group. Data are presented as the mean ± S.D. (n = 3, each group). b, Oxygen consumption rates (OCR) of mitochondrial maximal respiration quantified from the mitochondrial-stress test in (a) are shown. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. c, Mitochondrial DNA copy numbers in MEFs with SKO plus Glis1 or SKO plus Flag. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. d, Mitochondrial stress test using Seahorse XF24 analyzer on day 8. SKO plus shLuc as a control compared to SKO plus shGlis1, Flag as a control to all groups. Data are presented as the mean ± S.D. (n = 3, each group). e, Oxygen consumption rates (OCR) of mitochondrial maximal respiration quantified from the mitochondrial stress test in (d) are shown. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. f, Flow cytometry analysis of SSEA1 in MEFs transduced with SKO in reprogramming on day3. (n = 3, each group). g, SSEA1- cells were infected with retroviral Flag or Glis1. GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. h, Mitochondrial stress test using Seahorse XF24 analyzer on day 8. SSEA1- plus Flag as a control compared to SSEA1- plus Glis1. Data are presented as the mean ± S.D. (n = 3, each group). i, Oxygen consumption rates (OCR) of mitochondrial maximal respiration quantified from the mitochondrial stress test in (h) are shown. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. j, Glycolysis stress test of iPSCs by Seahorse XF24 analyzer. The resultant iPSCs of SKO plus Flag as a control compared to SKO plus Glis1. Data are presented as the mean ± S.D. (n = 3, each group). k, Extracellular acidification rates (ECAR) quantified from the glycolysis stress test in (j) are shown. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. l, Mitochondrial stress test of iPSCs by Seahorse XF24 analyzer. The resultant iPSCs of SKO plus Flag as a control compared to SKO plus Glis1. Data are presented as the mean ± S.D. (n = 3, each group). m, Oxygen consumption rates (OCR) of mitochondrial maximal respiration quantified from the mitochondrial stress test in l, are shown. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. n, Relative concentration of pentose phosphate pathway (PPP) metabolites and nucleotide-related molecules. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. o, Relative band densities of H3K27Ac upon Glis1 overexpression and knockdown were quantified using Image J. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. p, Western blot analysis of Pan Kla and H3K18la after 20 mM lactate supplementation and knockdown of Ldha. Data are presented as the mean ± S.D. n = 3 independent experiments were repeated with similar results. q, Relative band densities of Pan Kla and H3K18la upon Glis1 overexpression and knockdown were quantified using Image J. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test.

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Extended Data Fig. 5 Glis1 enhances reprogramming by glycolysis-driven acetyl-CoA production.

(a) Western blot analysis of H3K27me3, H3K9me3 after Glis1 overexpression or knockdown on day 8 during somatic reprogramming. (n = 1, each group). (b) The effect of acetate on cell proliferation at different concentration. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. (c) The effect of acetate on the level of acetyl-CoA at different concentrations. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. (d) RT-qPCR analysis for detecting the Acly knockdown efficiency in MEFs. (e) OG2 MEFs were infected with retroviral SKO plus shLuc or shAcly addition of acetate. GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. (f) OG2 MEFs were infected with retroviral SKO plus Flag or Glis1 addition of VPA (0.5 mM). GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test.(g) OG2 MEFs were infected with retroviral SKO plus shLuc or shGlis1 addition of VPA (0.5 mM). GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. (h) OG2 MEFs were infected with retroviral SKO plus Flag or Glis1 addition of TSA (1 nM). GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. (i) OG2 MEFs were infected with retroviral SKO plus shLuc or shGlis1 addition of TSA (1 nM). GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test.

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Extended Data Fig. 6 Glis1 increased histone lactylation and acetylation at Sall4 and Mycn loci promoting their activation.

(a) Genome views of H3K27Ac tag density at Sall4 and Mycn; red box on the tracks indicates H3K27Ac peaks. Scale bar, 2 kb. For IGV analysis, 1 replicate (n = 1, each group) was used for H3K27Ac analysis in ChIP-seq assay. n = 2 independent experiments were repeated with similar results.(b) ChIP–qPCR analysis of H3K27Ac at Sall4 and Mycn on day 8 in MEFs transduced with SKO plus Flag or Glis1. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. (c) ChIP–qPCR analysis of H3K27Ac at Oct4, Sall4 and Mycn on day 8 in MEFs transduced with SKO plus shLuc or shGlis1. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. (d) ChIP–qPCR analysis of Pan Kla and H3K18la at Oct4, Sall4 and Mycn on day 8 in MEFs transduced with SKO plus shLuc or shGlis1. Data are presented as the mean ± S.D. (Pan kla, n = 3; H3K18la, n=3–4 each group). Group differences are analyzed by the two-tailed Student’s t test.(e) ChIP–qPCR analysis of P300 at Oct4, Sall4, Mycn, Setbp1, Col1a1 and Col5a1 on day 8 in MEFs transduced with Flag or SKO plus Flag. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. (f) Time course of qPCR analysis of endo-Oct4, Sall4, Mycn in MEFs transduced with SKO plus Flag or Glis1. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test. (g) The number of peaks defined in each of the OC/CO categories. Two replicate (n = 2, each group) was used for ATAC assay. (h) Time courses of qPCR analyses of T and Eomes in MEFs infected with retroviral SKO plus Flag or Glis1. Data are presented as the mean ± S.D. (n = 3, each group). Group differences are analyzed by the two-tailed Student’s t test.

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Li, L., Chen, K., Wang, T. et al. Glis1 facilitates induction of pluripotency via an epigenome–metabolome–epigenome signalling cascade. Nat Metab 2, 882–892 (2020). https://doi.org/10.1038/s42255-020-0267-9

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