RESEARCH ARTICLE

Telomere-dependent and telomereindependent roles of RAP1 in regulating human stem cell homeostasis

  • Xing Zhang 1,2,6 ,
  • Zunpeng Liu 1,6 ,
  • Xiaoqian Liu 1 ,
  • Si Wang 2,3,7 ,
  • Yiyuan Zhang 3,6 ,
  • Xiaojuan He 2 ,
  • Shuhui Sun 3 ,
  • Shuai Ma 3 ,
  • Ng Shyh-Chang 1,6,7 ,
  • Feng Liu 5,6,7 ,
  • Qiang Wang 5,6,7 ,
  • Xiaoqun Wang 3,6,7 ,
  • Lin Liu 4 ,
  • Weiqi Zhang , 2,3,6,7 ,
  • Moshi Song , 5,6,7 ,
  • Guang-Hui Liu , 2,3,6,7,8,9 ,
  • Jing Qu , 1,6,7
Expand
  • 1. State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
  • 2. Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
  • 3. National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
  • 4. State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
  • 5. State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
  • 6. University of Chinese Academy of Sciences, Beijing 100049, China
  • 7. Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
  • 8. Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China
  • 9. Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China

Received date: 02 Dec 2018

Accepted date: 03 Jan 2019

Published date: 15 Sep 2019

Copyright

2019 The Author(s)

Abstract

RAP1 is a well-known telomere-binding protein, but its functions in human stem cells have remained unclear. Here we generated RAP1-deficient human embryonic stem cells (hESCs) by using CRISPR/Cas9 technique and obtained RAP1-deficient human mesenchymal stem cells (hMSCs) and neural stem cells (hNSCs) via direc- ted differentiation. In both hMSCs and hNSCs, RAP1 not only negatively regulated telomere length but also acted as a transcriptional regulator of RELN by tuning the methylation status of its gene promoter. RAP1 defi- ciency enhanced self-renewal and delayed senescence in hMSCs, but not in hNSCs, suggesting complicated lineage-specific effects of RAP1 in adult stem cells. Altogether, these results demonstrate for the first time that RAP1 plays both telomeric and nontelomeric roles in regulating human stem cell homeostasis.

Cite this article

Xing Zhang , Zunpeng Liu , Xiaoqian Liu , Si Wang , Yiyuan Zhang , Xiaojuan He , Shuhui Sun , Shuai Ma , Ng Shyh-Chang , Feng Liu , Qiang Wang , Xiaoqun Wang , Lin Liu , Weiqi Zhang , Moshi Song , Guang-Hui Liu , Jing Qu . Telomere-dependent and telomereindependent roles of RAP1 in regulating human stem cell homeostasis[J]. Protein & Cell, 2019 , 10(9) : 649 -667 . DOI: 10.1007/s13238-019-0610-7

1
Anders S, Pyl PT, Huber W (2015) HTSeq–a Python framework to work with high-throughput sequencing data. Nat Methods 31:166–169

DOI

2
Arnoult N, Van Beneden A, Decottignies A (2012) Telomere length regulates TERRA levels through increased trimethylation of telomeric H3K9 and HP1alpha. Nat Struct Mol Biol 19:948–956

DOI

3
Bandaria JN, Qin P, Berk V, Chu S, Yildiz A (2016) Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin. Cell 164:735–746

DOI

4
Blackburn EH (2001) Switching and signaling at the telomere. Cell 106:661–673

DOI

5
Blackburn EH, Epel ES, Lin J (2015) Human telomere biology: A contributory and interactive factor in aging, disease risks, and protection. Science 350:1193–1198

DOI

6
Bourgeron T, Xu Z, Doumic M, Teixeira MT (2015) The asymmetry of telomere replication contributes to replicative senescence heterogeneity. Sci Rep 5:15326

DOI

7
Calado RT, Dumitriu B (2013) Telomere dynamics in mice and humans. Semin Hematol 50:165–174

DOI

8
Cawthon RM (2002) Telomere measurement by quantitative PCR. Nucleic Acids Res 30:e47

DOI

9
Chen J, Bardes EE, Aronow BJ, Jegga AG (2009) ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic acids Res 37:W305–311

DOI

10
Dahl JA, Collas P (2008) A rapid micro chromatin immunoprecipitation assay (microChIP). Nat Protoc 3:1032–1045

DOI

11
Debacq-Chainiaux F, Erusalimsky JD, Campisi J, Toussaint O (2009) Protocols to detect senescence-associated beta-galactosidase (SA-betagal) activity, a biomarker of senescent cells in culture and in vivo. Nat Protoc 4:1798–1806

DOI

12
Di Palma T, Filippone MG, Pierantoni GM, Fusco A, Soddu S, Zannini M (2013) Pax8 has a critical role in epithelial cell survival and proliferation. Cell Death Dis 4:e729

DOI

13
Ding Y, Liang X, Zhang Y, Yi L, Shum HC, Chen Q, Chan BP, Fan H, Liu Z, Tergaonkar V (2018) Rap1 deficiency-provoked paracrine dysfunction impairs immunosuppressive potency of mesenchymal stem cells in allograft rejection of heart transplantation. Cell Death Dis 9:386

DOI

14
Doerks T, Copley RR, Schultz J, Ponting CP, Bork P (2002) Systematic identification of novel protein domain families associated with nuclear functions. Genome Res 12:47–56

DOI

15
Donato R, Sorci G, Giambanco I (2017) S100A6 protein: functional roles. Cell Mol Life Sci 74:2749–2760

DOI

16
Duan S, Yuan G, Liu X, Ren R, Li J, Zhang W, Wu J, Xu X, Fu L, Li Y (2015) PTEN deficiency reprogrammes human neural stem cells towards a glioblastoma stem cell-like phenotype. Nat Commun 6:10068

DOI

17
Feretzaki M, Lingner J (2017) A practical qPCR approach to detect TERRA, the elusive telomeric repeat-containing RNA. Methods 114:39–45

DOI

18
Ferrara-Romeo I, Martinez P, Blasco MA (2018) Mice lacking RAP1 show early onset and higher rates of DEN-induced hepatocellular carcinomas in female mice. PloS ONE 13:e0204909

DOI

19
Fu L, Xu X, Ren R, Wu J, Zhang W, Yang J, Ren X, Wang S, Zhao Y, Sun L (2016) Modeling xeroderma pigmentosum associated neurological pathologies with patients-derived iPSCs. Protein Cell 7:210–221

DOI

20
Geng L, Liu Z, Zhang W, Li W, Wu Z, Wang W, Ren R, Su Y, Wang P, Sun L (2018) Chemical screen identifies a geroprotective role of quercetin in premature aging. Protein Cell. https://doi.org/10.1007/s13238-018-0567-y

DOI

21
Goodell MA, Rando TA (2015) Stem cells and healthy aging. Science 350:1199–1204

DOI

22
Greider CW (1991) Telomeres. Curr Opin Cell Biol 3:444–451

DOI

23
Ha G, Roth A, Lai D, Bashashati A, Ding J, Goya R, Giuliany R, Rosner J, Oloumi A, Shumansky K (2012) Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer. Genome Res 22:1995–2007

DOI

24
Hohensinner PJ, Kaun C, Buchberger E, Ebenbauer B, Demyanets S, Huk I, Eppel W, Maurer G, Huber K, Wojta J (2016) Age intrinsic loss of telomere protection via TRF1 reduction in endothelial cells. Biochim Biophys Acta 1863:360–367

DOI

25
Ishii K, Kubo KI, Nakajima K (2016) Reelin and Neuropsychiatric Disorders. Front Cell Neurosci 10:229

DOI

26
Kabir S, Hockemeyer D, de Lange T (2014) TALEN gene knockouts reveal no requirement for the conservedhuman shelterin protein Rap1 in telomere protection and length regulation. Cell Rep 9:1273–1280

DOI

27
Kabir S, Sfeir A, de Lange T (2010) Taking apart Rap1: an adaptor protein with telomeric and non-telomeric functions. Cell cycle 9:4061–4067

DOI

28
Kanoh J, Ishikawa F (2001) spRap1 and spRif1, recruited to telomeres by Taz1, are essential for telomere function in fission yeast. Curr Biol 11:1624–1630

DOI

29
Khurana E, Fu Y, Chen J, Gerstein M (2013) Interpretation of genomic variants using a unified biological network approach. PLoS Comput Biol 9:e1002886

DOI

30
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360

DOI

31
Kim H, Li F, He Q, Deng T, Xu J, Jin F, Coarfa C, Putluri N, Liu D, Songyang Z (2017) Systematic analysis of human telomeric dysfunction using inducible telosome/shelterin CRISPR/Cas9 knockout cells. Cell Discov 3:17034

DOI

32
Kubben N, Zhang W, Wang L, Voss TC, Yang J, Qu J, Liu GH, Misteli T (2016) Repression of the antioxidant NRF2 pathway in premature aging. Cell 165:1361–1374

DOI

33
Kundakovic M, Chen Y, Costa E, Grayson DR (2007) DNA methyltransferase inhibitors coordinately induce expression of the human reelin and glutamic acid decarboxylase 67 genes. Mol Pharmacol 71:644–653

DOI

34
Kundakovic M, Chen Y, Guidotti A, Grayson DR (2009) The reelin and GAD67 promoters are activated by epigenetic drugs that facilitate the disruption of local repressor complexes. Mol Pharmacol 75:342–354

DOI

35
Kyrion G, Liu K, Liu C, Lustig AJ (1993) RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae. Genes Dev 7:1146–1159

DOI

36
Lai TP, Wright WE, Shay JW (2016) Generation of digoxigeninincorporated probes to enhance DNA detection sensitivity. BioTechniques 60:306–309

DOI

37
Lancaster MA, Knoblich JA (2014) Generation of cerebral organoids from human pluripotent stem cells. Nat Protoc 9:2329–2340

DOI

38
Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP, Knoblich JA (2013) Cerebral organoids model human brain development and microcephaly. Nature 501:373–379

DOI

39
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

DOI

40
Lensch MW, Schlaeger TM, Zon LI, Daley GQ (2007) Teratoma formation assays with human embryonic stem cells: a rationale for one type of human-animal chimera. Cell Stem Cell 1:253–258

DOI

41
Li B, de Lange T (2003) Rap1 affects the length and heterogeneity of human telomeres. Mol Biol Cell 14:5060–5068

DOI

42
Li WP, Liu P, Pilcher BK, Anderson RG (2001) Cell-specific targeting of caveolin-1 to caveolae, secretory vesicles, cytoplasm or mitochondria. J Cell Sci 114:1397–1408

43
Lintas C, Sacco R, Persico AM (2016) Differential methylation at the RELN gene promoter in temporal cortex from autistic and typically developing post-puberal subjects. J Neurodev Disord 8:18

DOI

44
Liu GH, Barkho BZ, Ruiz S, Diep D, Qu J, Yang SL, Panopoulos AD, Suzuki K, Kurian L, Walsh C (2011) Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. Nature 472:221–225

DOI

45
Liu GH, Suzuki K, Li M, Qu J, Montserrat N, Tarantino C, Gu Y, Yi F, Xu X, Zhang W (2014) Modelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs. Nat Commun 5:4330

DOI

46
Londono-Vallejo JA (2004) Telomere length heterogeneity and chromosome instability. Cancer letters 212:135–144

DOI

47
Lopez-Otin C, Blasco MA, Partridge L, Serrano M, Kroemer G (2013) The hallmarks of aging. Cell 153:1194–1217

DOI

48
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550

DOI

49
Luo K, Vega-Palas MA, Grunstein M (2002) Rap1-Sir4 binding independent of other Sir, yKu, or histone interactions initiates the assembly of telomeric heterochromatin in yeast. Genes Dev 16:1528–1539

DOI

50
Martinez P, Gomez-Lopez G, Garcia F, Mercken E, Mitchell S, Flores JM, de Cabo R, Blasco MA (2013) RAP1 protects from obesity through its extratelomeric role regulating gene expression. Cell reports 3:2059–2074

DOI

51
Martinez P, Gomez-Lopez G, Pisano DG, Flores JM, Blasco MA (2016) A genetic interaction between RAP1 and telomerase reveals an unanticipated role for RAP1 in telomere maintenance. Aging Cell 15(6):1113–1125

DOI

52
Martinez P, Thanasoula M, Carlos AR, Gomez-Lopez G, Tejera AM, Schoeftner S, Dominguez O, Pisano DG, Tarsounas M, Blasco MA (2010) Mammalian Rap1 controls telomere function and gene expression through binding to telomeric and extratelomeric sites. Nat Cell Biol 12:768–780

DOI

53
Moretti P, Shore D (2001) Multiple interactions in Sir protein recruitment by Rap1p at silencers and telomeres in yeast. Molecular and cellular biology 21:8082–8094

DOI

54
Nabil Fikri RM, Norlelawati AT, Nour El-Huda AR, Hanisah MN, Kartini A, Norsidah K, Nor Zamzila A (2017) Reelin (RELN) DNA methylation in the peripheral blood of schizophrenia. J Psychiatr Res 88:28–37

DOI

55
Nanavaty V, Sandhu R, Jehi SE, Pandya UM, Li B (2017) Trypanosoma brucei RAP1 maintains telomere and subtelomere integrity by suppressing TERRA and telomeric RNA:DNA hybrids. Nucleic Acids Res 45:5785–5796

DOI

56
O’Connor MS, Safari A, Liu D, Qin J, Songyang Z (2004) The human Rap1 protein complex and modulation of telomere length. The Journal of biological chemistry 279:28585–28591

DOI

57
Omura N, Li CP, Li A, Hong SM, Walter K, Jimeno A, Hidalgo M, Goggins M(2008) Genome-wide profiling of methylated promoters in pancreatic adenocarcinoma. Cancer Biol Ther 7:1146–1156

DOI

58
Palm W, de Lange T (2008) How shelterin protects mammalian telomeres. Annu Rev Genet 42:301–334

DOI

59
Pan H, Guan D, Liu X, Li J, Wang L, Wu J, Zhou J, Zhang W, Ren R, Zhang W (2016) SIRT6 safeguards human mesenchymal stem cells from oxidative stress by coactivating NRF2. Cell Res 26:190–205

DOI

60
Proctor CJ, Kirkwood TB (2003) Modelling cellular senescence as a result of telomere state. Aging cell 2:151–157

DOI

61
Reddel RR (2014) Telomere maintenance mechanisms in cancer: clinical implications. Curr Pharm Des 20:6361–6374

DOI

62
Ren R, Deng L, Xue Y, Suzuki K, Zhang W, Yu Y, Wu J, Sun L, Gong X, Luan H (2017a) Visualization of aging-associated chromatin alterations with an engineered TALE system. Cell Res 27:483–504

DOI

63
Ren R, Ocampo A, Liu GH, Izpisua Belmonte JC (2017b) Regulation of stem cell aging by metabolism and epigenetics. Cell Metab 26:460–474

DOI

64
Sato N, Fukushima N, Chang R, Matsubayashi H, Goggins M (2006) Differential and epigenetic gene expression profiling identifies frequent disruption of the RELN pathway in pancreatic cancers. Gastroenterology 130:548–565

DOI

65
Schmutz I, de Lange T (2016) Shelterin. Curr Biol 26:R397–399

DOI

66
Schulze M, Violonchi C, Swoboda S, Welz T, Kerkhoff E, Hoja S, Bruggemann S, Simburger J, Reinders J, Riemenschneider MJ (2017) RELN signaling modulates glioblastoma growth and substrate-dependent migration. Brain Pathol 28(5):695–709

DOI

67
Sekine K, Kubo K, Nakajima K (2014) How does Reelin control neuronal migration and layer formation in the developing mammalian neocortex? Neurosci Res 86:50–58

DOI

68
Sfeir A, Kabir S, van Overbeek M, Celli GB, de Lange T (2010) Loss of Rap1 induces telomere recombination in the absence of NHEJ or a DNA damage signal. Science 327:1657–1661

DOI

69
Shore D, Nasmyth K (1987) Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements. Cell 51:721–732

DOI

70
Smogorzewska A, de Lange T (2004) Regulation of telomerase by telomeric proteins. Annu Rev Biochem 73:177–208

DOI

71
Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131:861–872

DOI

72
Vincent A, Omura N, Hong SM, Jaffe A, Eshleman J, Goggins M (2011) Genome-wide analysis of promoter methylation associated with gene expression profile in pancreatic adenocarcinoma. Clin Cancer Res 17:4341–4354

DOI

73
Wagner KD, Ying Y, Leong W, Jiang J, Hu X, Chen Y, Michiels JF, Lu Y, Gilson E, Wagner N (2017) The differential spatiotemporal expression pattern of shelterin genes throughout lifespan. Aging 9:1219–1232

DOI

74
Wang P, Liu Z, Zhang X, Li J, Sun L, Ju Z, Li J, Chan P, Liu GH, Zhang W (2018a) CRISPR/Cas9-mediated gene knockout reveals a guardian role of NF-kappaB/RelA in maintaining the homeostasis of human vascular cells. Protein Cell 9(11):945–965

DOI

75
Wang S, Hu B, Ding Z, Dang Y, Wu J, Li D, Liu X, Xiao B, Zhang W, Ren R (2018b) ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells. Cell Discov 4:2

DOI

76
Wu Z, Zhang W, Song M, Wang W, Wei G, Li W, Lei J, Huang Y, Sang Y, Chan P (2018) Differential stem cell aging kinetics in Hutchinson-Gilford progeria syndrome and Werner syndrome. Protein Cell 9:333–350

DOI

77
Xiao L, Lan X, Shi X, Zhao K, Wang D, Wang X, Li F, Huang H, Liu J (2017) Cytoplasmic RAP1 mediates cisplatin resistance of nonsmall cell lung cancer. Cell Death Dis 8:e2803

DOI

78
Xin H, Liu D, Songyang Z (2008) The telosome/shelterin complex and its functions. Genome Biol 9:232

DOI

79
Xu Z, Duc KD, Holcman D, Teixeira MT (2013) The length of the shortest telomere as the major determinant of the onset of replicative senescence. Genetics 194:847–857

DOI

80
Yang D, Xiong Y, Kim H, He Q, Li Y, Chen R, Songyang Z (2011) Human telomeric proteins occupy selective interstitial sites. Cell Res 21:1013–1027

DOI

81
Yang J, Li J, Suzuki K, Liu X, Wu J, Zhang W, Ren R, Zhang W, Chan P, Izpisua Belmonte JC (2017) Genetic enhancement in cultured human adult stem cells conferred by a single nucleotide recoding. Cell Res 27:1178–1181

DOI

82
Yang X, Figueiredo LM, Espinal A, Okubo E, Li B (2009) RAP1 is essential for silencing telomeric variant surface glycoprotein genes in Trypanosoma brucei. Cell 137:99–109

DOI

83
Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science 318:1917–1920

DOI

84
Zha Y, Gan P, Yao Q, Ran FM, Tan J (2014) Downregulation of Rap1 promotes 5-fluorouracil-induced apoptosis in hepatocellular carcinoma cell line HepG2. Oncol Rep 31:1691–1698

DOI

85
Zhang W, Li J, Suzuki K, Qu J, Wang P, Zhou J, Liu X, Ren R, Xu X, Ocampo A (2015) Aging stem cells. A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging. Science 348:1160–1163

DOI

86
Zhang W, Wan H, Feng G, Qu J,Wang J, Jing Y, Ren R, Liu Z, Zhang L, Chen Z (2018) SIRT6 deficiency results in developmental retardation in cynomolgus monkeys. Nature 560:661–665

DOI

87
Zhu Y, Liu X, Ding X, Wang F, Geng X (2018) Telomere and its role in the aging pathways: telomere shortening, cell senescence and mitochondria dysfunction. Biogerontology 20:1–16

DOI

Outlines

/