#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

microRNAs Regulate Cell-to-Cell Variability of Endogenous Target Gene Expression in Developing Mouse Thymocytes


microRNAs are integral to many developmental processes and may 'canalise' development by reducing cell-to-cell variation in gene expression. This idea is supported by computational studies that have modeled the impact of microRNAs on the expression of their targets and the construction of artificial incoherent feedforward loops using synthetic biology tools. Here we show that this interesting principle of microRNA regulation actually occurs in a mammalian developmental system. We examine cell-to-cell variation of protein expression in developing mouse thymocytes by quantitative flow cytometry and find that the absence of microRNAs results in increased cell-to-cell variation in the expression of the microRNA target Cd69. Mechanistically, T cell receptor signaling induces both Cd69 and miR-17 and miR-20a, two microRNAs that target Cd69. Co-regulation of microRNAs and their target mRNA dampens the expression of Cd69 and forms an incoherent feedforward loop that reduces cell-to-cell variation on CD69 expression. In addition, miR-181, which also targets Cd69 and is a known modulator of T cell receptor signaling, also affects cell-to-cell variation of CD69 expression. The ability of microRNAs to control the uniformity of gene expression across mammalian cell populations may be important for normal development and for disease.


Vyšlo v časopise: microRNAs Regulate Cell-to-Cell Variability of Endogenous Target Gene Expression in Developing Mouse Thymocytes. PLoS Genet 11(2): e32767. doi:10.1371/journal.pgen.1005020
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005020

Souhrn

microRNAs are integral to many developmental processes and may 'canalise' development by reducing cell-to-cell variation in gene expression. This idea is supported by computational studies that have modeled the impact of microRNAs on the expression of their targets and the construction of artificial incoherent feedforward loops using synthetic biology tools. Here we show that this interesting principle of microRNA regulation actually occurs in a mammalian developmental system. We examine cell-to-cell variation of protein expression in developing mouse thymocytes by quantitative flow cytometry and find that the absence of microRNAs results in increased cell-to-cell variation in the expression of the microRNA target Cd69. Mechanistically, T cell receptor signaling induces both Cd69 and miR-17 and miR-20a, two microRNAs that target Cd69. Co-regulation of microRNAs and their target mRNA dampens the expression of Cd69 and forms an incoherent feedforward loop that reduces cell-to-cell variation on CD69 expression. In addition, miR-181, which also targets Cd69 and is a known modulator of T cell receptor signaling, also affects cell-to-cell variation of CD69 expression. The ability of microRNAs to control the uniformity of gene expression across mammalian cell populations may be important for normal development and for disease.


Zdroje

1. Waddington C. H. (1959). Canalization of development and genetic assimilation of acquired characters. Nature 183: 1634–1638 13666845

2. Hornstein E., Shomron N. (2006). Canalization of development by microRNAs. Nat. Genet. 38: S20–S24. 16736020

3. Tsang J, Zhu J, van Oudenaarden A. 2007. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 26: 753–767. 17560377

4. Herranz H., Cohen S. M. (2010). MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems. Genes Dev. 24: 1339–1344. doi: 10.1101/gad.1937010 20595229

5. Ebert M. S., Sharp P. A. (2012) Roles for microRNAs in conferring robustness to biological processes. Cell 149: 515–524. doi: 10.1016/j.cell.2012.04.005 22541426

6. Mangan S, Alon U. (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA. 100: 11980–11985 14530388

7. Bleris L., Xie Z, Glass D, Adadey A, Sontag E, et al. (2011) Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template. Mol. Syst. Biol. 7: 519. doi: 10.1038/msb.2011.49 21811230

8. Osella M, Bosia C, Corá D, Caselle M. (2011) The Role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput Biol. 7: e1001101. doi: 10.1371/journal.pcbi.1001101 21423718

9. Swain PS, Elowitz MB, Siggia ED (2002). Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A. 99: 12795–12800. 12237400

10. Siciliano V, Garzilli I, Fracassi C, Criscuolo S, Ventre S, et al. (2013) miRNAs confer phenotypic robustness to gene networks by suppressing biological noise. Nat Commun. 4: 2364. doi: 10.1038/ncomms3364 24077216

11. Li X., Cassidy J. J., Reinke C. A., Fischboeck S. Carthew R. W. (2009) A microRNA imparts robustness against environmental fluctuation during development. Cell 137: 273–282. doi: 10.1016/j.cell.2009.01.058 19379693

12. Yohn C. B., Pusateri L., Barbosa V., and Lehmann R. (2003) Malignant brain tumor and three novel genes are required for Drosophila germ-cell formation. Genetics 165: 1889–1900. 14704174

13. Kugler JM, Chen YW, Weng R, Cohen SM. (2013) Maternal loss of miRNAs leads to increased variance in primordial germ cell numbers in Drosophila melanogaster. G3 (Bethesda). 3: 1573–1576. doi: 10.1534/g3.113.007591 23893743

14. Li Y, Wang F, Lee JA, Gao FB. (2006) MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila. Genes Dev. 20: 2793–805. 17015424

15. Arif S., Murat S., Almudi I., Nunes M. D., Bortolamiol-Becet D., et al. (2013) Evolution of mir-92a underlies natural morphological variation in Drosophila melanogaster. Curr Biol. 23: 523–528. doi: 10.1016/j.cub.2013.02.018 23453955

16. Cohen SM, Brennecke J, Stark A. (2006) Denoising feedback loops by thresholding—a new role for microRNAs. Genes Dev. 20: 2769–2772. 17043305

17. Dill H., Linder B., Fehr A., and Fischer U. (2012). Intronic miR-26b controls neuronal differentiation by repressing its host transcript, ctdsp2. Genes Dev. 26: 25–30. doi: 10.1101/gad.177774.111 22215807

18. Dh Kim, Grün D, van Oudenaarden A. (2013). Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Nat Genet. 45: 1337–1344 doi: 10.1038/ng.2763 24036951

19. Nakamoto M, Jin P, O'Donnell WT, Warren ST (2005) Physiological identification of human transcripts translationally regulated by a specific microRNA. Hum Mol Genet 14: 3813–3821. 16239240

20. Klein M.E., Lioy D.T., Ma L., Impey S., Mandel G, et al. (2007). Homeostatic regulation of MeCP2 expression by a CREB-induced microRNA. Nat. Neurosci. 10: 1513–1514 17994015

21. Ghosh T, Aprea J, Nardelli J, Engel H, Selinger C, et al. (2014). MicroRNAs establish robustness and adaptability of a critical gene network to regulate progenitor fate decisions during cortical neurogenesis. Cell Reports 7: 1779–1788. doi: 10.1016/j.celrep.2014.05.029 24931612

22. Bian S, Hong J, Li Q, Schebelle L., Pollock A, et al. (2013). MicroRNA cluster miR-17-92 regulates neural stem cell expansion and transition to intermediate progenitors in the developing mouse neocortex. Cell Reports, 3, 1398–1406. doi: 10.1016/j.celrep.2013.03.037 23623502

23. Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, et al. (2014). Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 516: 56–61. doi: 10.1038/nature13920 25471879

24. Kisielow P, von Boehmer H. (1995). Development and selection of T cells: facts and puzzles. Adv Immunol. 58: 87–209. 7741032

25. Feinerman O, Veiga J, Dorfman JR, Germain RN, Altan-Bonnet G. (2008) Variability and robustness in T cell activation from regulated heterogeneity in protein levels. Science 321: 1081–1084. doi: 10.1126/science.1158013 18719282

26. Cobb BS, Nesterova TB, Thompson E, Hertweck A, O'Connor E, et al. (2005). T cell lineage choice and differentiation in the absence of the RNAse III enzyme dicer. J. Exp. Med. 201: 1367–1373 15867090

27. Sood P, Krek A, Zavolan M, Macino G, Rajewsky N. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A. 2006. 103: 2746–2751. 16477010

28. Liu C, Kelnar K, Liu B, Chen X, Calhoun-Davis T, et al. (2011) The microRNA miR-34a inhibits prostate cancer stem cells and metastasis by directly repressing CD44. Nat Med. 17: 211–215. doi: 10.1038/nm.2284 21240262

29. Sancho D, Gomez M, Sanchez-Madrid F (2005) CD69 is an immunoregulatory molecule induced following activation. Trends in Immunology 26: 136–140 15745855

30. Shiow LR, Rosen DB, Brdickova N, Xu Y, An J, et al. (2006) CD69 acts downstream of interferon-alpha/beta to inhibit S1P1 and lymphocyte egress from lymphoid organs. Nature 440: 540–544 16525420

31. Neilson JR, Zheng GX, Burge CB, Sharp PA. (2007) Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev. 21: 578–589. 17344418

32. Zhang N, Bevan MJ. (2010) Dicer controls CD8+ T-cell activation, migration, and survival. Proc Natl Acad Sci U S A. 107: 21629–21634. doi: 10.1073/pnas.1016299107 21098294

33. de Kouchkovsky D, Esensten JH, Rosenthal WL, Morar MM, Bluestone JA, et al. (2013) microRNA-17-92 regulates IL-10 production by regulatory T cells and control of experimental autoimmune encephalomyelitis. J Immunol. 191: 1594–605. doi: 10.4049/jimmunol.1203567 23858035

34. Tanzer A, Stadler PF. (2004) Molecular evolution of a microRNA cluster. J Mol Biol. 339: 327–335. 15136036

35. Cobb BS, Hertweck A, Smith J, O'Connor E, Graf D, et al. (2006). A role for Dicer in immune regulation. J. Exp. Med. 203: 2519–2527. 17060477

36. Fragoso R, Mao T, Wang S, Schaffert S, Gong X, et al. (2012). Modulating the strength and threshold of NOTCH oncogenic signals by mir-181a-1/b-1. PLoS Genet. 8: e1002855. doi: 10.1371/journal.pgen.1002855 22916024

37. Li QJ, Chau J, Ebert PJ, Sylvester G, Min H, et al. (2007) miR-181a is an intrinsic modulator of T cell sensitivity and selection. Cell 129: 147–161 17382377

38. Ebert PJ, Jiang S, Xie J, Li QJ, Davis MM. (2009) An endogenous positively selecting peptide enhances mature T cell responses and becomes an autoantigen in the absence of microRNA miR-181a. Nat. Immunol. 10: 1162–1169 doi: 10.1038/ni.1797 19801983

39. Haasch D, Chen YW, Reilly RM, Chiou XG, Koterski S, et al. (2002) T cell activation induces a noncoding RNA transcript sensitive to inhibition by immunosuppressant drugs and encoded by the proto-oncogene, BIC. Cell Immunol. 217: 78–86. 12426003

40. Monticelli S, Ansel KM, Xiao C, Socci ND, Krichevsky AM, et al. (2005). MicroRNA profiling of the murine hematopoietic system. Genome Biol. 6: R71. 16086853

41. Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, et al. (2009). Chromatin poises miRNA- and protein-coding genes for expression. Genome Res. 19: 1742–1751. doi: 10.1101/gr.090951.109 19713549

42. Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. (2008) Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science. 320: 1643–1647. doi: 10.1126/science.1155390 18566288

43. Jiang S, Li C, Olive V, Lykken E, Feng F, et al. (2011) Molecular dissection of the miR-17-92 cluster's critical dual roles in promoting Th1 responses and preventing inducible Treg differentiation. Blood 118: 5487–5497. doi: 10.1182/blood-2011-05-355644 21972292

44. Wu H, Neilson JR, Kumar P, Manocha M, Shankar P, et al. (2007). miRNA profiling of naïve, effector and memory CD8 T cells. PLoS One. 2: e1020. 17925868

45. Bronevetsky Y, Villarino AV, Eisley CJ, Barbeau R, Barczak AJ, et al. (2013) T cell activation induces proteasomal degradation of Argonaute and rapid remodeling of the microRNA repertoire. J Exp Med. 210: 417–432. doi: 10.1084/jem.20111717 23382546

46. Kelly K, Siebenlist U. (1988). Mitogenic activation of normal T cells leads to increased initiation of transcription in the c-myc locus. J Biol Chem. 263: 4828–4831. 3127392

47. Patrussi L, Savino MT, Pellegrini M, Paccani SR, Migliaccio E, et al. (2005) Cooperation and selectivity of the two Grb2 binding sites of p52Shc in T-cell antigen receptor signaling to Ras family GTPases and Myc-dependent survival. Oncogene 24: 2218–2228 15688026

48. O'Donnell K.A., Wentzel E.A., Zeller K.I., Dang C.V., Mendell J.T. (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435: 839–843. 15944709

49. Mukherji S, Ebert MS, Zheng GX, Tsang JS, Sharp PA, et al. (2011). MicroRNAs can generate thresholds in target gene expression. Nat Genet. 43: 854–859. doi: 10.1038/ng.905 21857679

50. Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H, et al. (2003) Dicer is essential for mouse development. Nat Genet. 35: 215–217. 14528307

51. Raser J.M., and O’Shea E.K. (2005). Noise in gene expression: origins, consequences, and control. Science 309: 2010–2013. 16179466

52. Gascoigne NR, Palmer E. (2011). Signaling in thymic selection. Curr Opin Immunol. 23: 207–212 doi: 10.1016/j.coi.2010.12.017 21242076

53. Muljo SA, Ansel KM, Kanellopoulou C, Livingston DM, Rao A, et al. (2005) Aberrant T cell differentiation in the absence of Dicer. J Exp Med. 202: 261–269. 16009718

54. Lu LF, Boldin MP, Chaudhry A, Lin LL, Taganov KD, et al. (2010) Function of miR-146a in controlling Treg cell-mediated regulation of Th1 responses. Cell 142: 914–929. doi: 10.1016/j.cell.2010.08.012 20850013

55. Henao-Mejia J, Williams A, Goff LA, Staron M, Licona-Limón P, et al. (2013). The microRNA miR-181 is a critical cellular metabolic rheostat essential for NKT cell ontogenesis and lymphocyte development and homeostasis. Immunity 38: 984–997. doi: 10.1016/j.immuni.2013.02.021 23623381

56. Ziętara N, Łyszkiewicz M, Witzlau K, Naumann R, Hurwitz R, et al. (2013) Critical role for miR-181a/b-1 in agonist selection of invariant natural killer T cells. Proc Natl Acad Sci USA 110: 7407–7412. doi: 10.1073/pnas.1221984110 23589855

57. Rupp LJ, Brady BL, Carpenter AC, De Obaldia ME, Bhandoola A, et al. (2014) The microRNA Biogenesis Machinery Modulates Lineage Commitment during αβ T Cell Development. J Immunol. 193: 4032–4042. doi: 10.4049/jimmunol.1401359 25217159

58. Sauer S, Bruno L, Hertweck A, Finlay D, Leleu M, et al. (2008) T cell receptor signaling controls Foxp3 expression via PI3K, Akt, and mTOR. Proc Natl Acad Sci USA 105: 7797–7802. doi: 10.1073/pnas.0800928105 18509048

59. Merkenschlager M, Graf D, Lovatt M, Bommhardt U, Zamoyska R, et al. (1997) How many thymocytes audition for selection? J Exp Med. 186: 1149–1158. 9314563

60. Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, et al. (2014). RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 42: D756–63. doi: 10.1093/nar/gkt1114 24259432

61. Kozomara A, Griffiths-Jones S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 42: D68–73. doi: 10.1093/nar/gkt1181 24275495

62. Wöbke TK, von Knethen A, Steinhilber D, Sorg BL (2013). CD69 is a TGF-β/1α,25-dihydroxyvitamin D3 target gene in monocytes. PLoS One 8: e64635. doi: 10.1371/journal.pone.0064635 23696902

63. Battich N, Stoeger T, Pelkmans L (2013). Image-based transcriptomics in thousands of single human cells at single-molecule resolution. Nat Methods 10: 1127–1133. doi: 10.1038/nmeth.2657 24097269

64. Kirigin FF, Lindstedt K, Sellars M, Ciofani M, Low SL, et al. (2012) Dynamic microRNA gene transcription and processing during T cell development. J Immunol. 188: 3257–3267. doi: 10.4049/jimmunol.1103175 22379031

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2015 Číslo 2
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Aktuální možnosti diagnostiky a léčby litiáz
nový kurz
Autori: MUDr. Tomáš Ürge, PhD.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#