A minimal fate-selection switch

Current Opinion in Cell Biology

Volumn 37, Issue , 2015, Pages 111-118

  Weinberger, Leor S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BET HEDGING CIRCUIT; CELL FATE; CELL SELECTION; GENE EXPRESSION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; NONHUMAN; PRIORITY JOURNAL; REVIEW; VIRAL PHENOMENA AND FUNCTIONS; VIRUS LATENCY; VIRUS REPLICATION; VIRUS TRANSMISSION; CELL LINEAGE; EVOLUTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; PHENOTYPE; PHYSIOLOGY; TRANSMISSION;

BIOLOGICAL EVOLUTION; CELL LINEAGE; HIV; HIV INFECTIONS; HUMANS; PHENOTYPE; VIRUS LATENCY;

EID: 84949731365     PISSN: 09550674     EISSN: 18790410     Source Type: Journal    
DOI: 10.1016/j.ceb.2015.10.005     Document Type: Review

References (49)

1. Elowitz M.B., Levine A.J., Siggia E.D., Swain P.S. Stochastic gene expression in a single cell. Science 2002, 297:1183-1186.
2. Endres R.G., Wingreen N.S. Precise adaptation in bacterial chemotaxis through assistance neighborhoods. Proc Natl Acad Sci U S A 2006, 103:13040-13044.
3. Rao C.V., Kirby J.R., Arkin A.P. Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol 2004, 2:E49.
4. Macnab R.M., Koshland D.E. The gradient-sensing mechanism in bacterial chemotaxis. Proc Natl Acad Sci U S A 1972, 69:2509-2512.
5. Muzzey D., Gomez-Uribe C.A., Mettetal J.T., van Oudenaarden A. A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell 2009, 138:160-171.
6. Cohen D. Optimizing reproduction in a randomly varying environment. J Theor Biol 1966, 12:119-129.
7. Arkin A., Ross J., McAdams H.H. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 1998, 149:1633-1648.
8. Raj A., van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 2008, 135:216-226.
9. Weinberger L.S., Burnett J.C., Toettcher J.E., Arkin A.P., Schaffer D.V. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 2005, 122:169-182.
10. Suel G.M., Kulkarni R.P., Dworkin J., Garcia-Ojalvo J., Elowitz M.B. Tunability and noise dependence in differentiation dynamics. Science 2007, 315:1716-1719.
11. Chang H.H., Hemberg M., Barahona M., Ingber D.E., Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 2008, 453:544-547.
12. Hanna J., Saha K., Pando B., van Zon J., Lengner C.J., Creyghton M.P., van Oudenaarden A., Jaenisch R. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 2009, 462:595-601.
13. Gupta P.B., Fillmore C.M., Jiang G., Shapira S.D., Tao K., Kuperwasser C., Lander E.S. Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell 2011, 146:633-644.
14. Siliciano R.F., Greene W.C. HIV latency. Cold Spring Harb Perspect Med 2011, 1:a007096.
15. Coffin J., Swanstrom R. HIV pathogenesis: dynamics and genetics of viral populations and infected cells. Cold Spring Harb Perspect Med 2013, 3:a012526.
16. Coffin J., Swanstrom R. HIV pathogenesis: dynamics and genetics of viral populations and infected cells. Cold Spring Harbor Perspect Med 2013, 3:a012526.
17. Han Y., Wind-Rotolo M., Yang H.C., Siliciano J.D., Siliciano R.F. Experimental approaches to the study of HIV-1 latency. Nat Rev Microbiol 2007, 5:95-106.
18. Eisele E., Siliciano R.F. Redefining the viral reservoirs that prevent HIV-1 eradication. Immunity 2012, 37:377-388.
19. Whitney J.B., Hill A., Sanisetty S., Penaloza-MacMaster P., Liu J., Shetty M., Parenteau L., Cabral C., Shields J., Blackmore S., et al. Rapid seeding of the viral reservoir prior to SIV viraemia in rhesus monkeys. Nature 2014, 512:74-77.
20. Ho Y.C., Shan L., Hosmane N.N., Wang J., Laskey S.B., Rosenbloom D.I., Lai J., Blankson J.N., Siliciano J.D., Siliciano R.F. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 2013, 155:540-551.
21. Weinberger A.D., Weinberger L.S. Stochastic fate selection in HIV-infected patients. Cell 2013, 155:497-499.
22. Dahabieh M.S., Ooms M., Simon V., Sadowski I. A doubly fluorescent HIV-1 reporter shows that the majority of integrated HIV-1 is latent shortly after infection. J Virol 2013, 87:4716-4727.
23. Calvanese V., Chavez L., Laurent T., Ding S., Verdin E. Dual-color HIV reporters trace a population of latently infected cells and enable their purification. Virology 2013, 446:283-292.
24. Weinberger L.S., Dar R.D., Simpson M.L. Transient-mediated fate determination in a transcriptional circuit of HIV. Nat Genet 2008, 40:466-470.
25. Burnett J.C., Miller-Jensen K., Shah P.S., Arkin A.P., Schaffer D.V. Control of stochastic gene expression by host factors at the HIV promoter. PLoS Pathogens 2009, 5:e1000260.
26. Rouzine I.M., Weinberger A.D., Weinberger L.S. An evolutionary role for HIV latency in enhancing viral transmission. Cell 2015, 160:1002-1012.
27. Haase A.T. Early events in sexual transmission of HIV and SIV and opportunities for interventions. Annu Rev Med 2011, 62:127-139.
28. Santiago M.L., Range F., Keele B.F., Li Y., Bailes E., Bibollet-Ruche F., Fruteau C., Noe R., Peeters M., Brookfield J.F., et al. Simian immunodeficiency virus infection in free-ranging sooty mangabeys (Cercocebus atys atys) from the Tai Forest, Cote d'Ivoire: implications for the origin of epidemic human immunodeficiency virus type 2. J Virol 2005, 79:12515-12527.
29. Zhang Z., Schuler T., Zupancic M., Wietgrefe S., Staskus K.A., Reimann K.A., Reinhart T.A., Rogan M., Cavert W., Miller C.J., et al. Sexual transmission and propagation of SIV and HIV in resting and activated CD4+ T cells. Science 1999, 286:1353-1357.
30. Nowak M., May R. Virus Dynamics: Mathematical Principles of Immunology and Virology 2000, Oxford University Press.
31. Deymier M.J., Ende Z., Fenton-May A.E., Dilernia D.A., Kilembe W., Allen S.A., Borrow P., Hunter E. Heterosexual transmission of subtype C HIV-1 selects consensus-like variants without increased replicative capacity or interferon-alpha resistance. PLoS Pathog 2015, 11:e1005154.
32. Tyagi M., Pearson R.J., Karn J. Establishment of HIV latency in primary CD4+ cells is due to epigenetic transcriptional silencing and P-TEFb restriction. J Virol 2010, 84:6425-6437.
33. Pearson R., Kim Y.K., Hokello J., Lassen K., Friedman J., Tyagi M., Karn J. Epigenetic silencing of human immunodeficiency virus (HIV) transcription by formation of restrictive chromatin structures at the viral long terminal repeat drives the progressive entry of HIV into latency. J Virol 2008, 82:12291-12303.
34. Jeeninga R.E., Westerhout E.M., van Gerven M.L., Berkhout B. HIV-1 latency in actively dividing human T cell lines. Retrovirology 2008, 5:37.
35. Razooky B.S., Pai A., Aull K., Rouzine I.M., Weinberger L.S. A hardwired HIV latency program. Cell 2015, 160:990-1001.
36. Singh A., Razooky B., Cox C.D., Simpson M.L., Weinberger L.S. Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression. Biophys J 2010, 98:L32-L34.
37. Singh A., Razooky B.S., Dar R.D., Weinberger L.S. Dynamics of protein noise can distinguish between alternate sources of gene-expression variability. Mol Syst Biol 2012, 8:607.
38. Dar R.D., Razooky B.S., Singh A., Trimeloni T.V., McCollum J.M., Cox C.D., Simpson M.L., Weinberger L.S. Transcriptional burst frequency and burst size are equally modulated across the human genome. Proc Natl Acad Sci U S A 2012, 109:17454-17459.
39. Weinberger L.S., Shenk T. An HIV feedback resistor: auto-regulatory circuit deactivator and noise buffer. PLoS Biol 2007, 5:e9.
40. Razooky B.S., Weinberger L.S. Mapping the architecture of the HIV-1 Tat circuit: a decision-making circuit that lacks bistability and exploits stochastic noise. Methods 2011, 53:68-77.
41. Fraser H.B., Hirsh A.E., Giaever G., Kumm J., Eisen M.B. Noise minimization in eukaryotic gene expression. PLoS Biol 2004, 2:e137.
42. Batada N.N., Hurst L.D. Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 2007, 39:945-949.
43. Brandman O., Ferrell J.E., Li R., Meyer T. Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 2005, 310:496-498.
44. Rouzine I.M., Razooky B.S., Weinberger L.S. Stochastic variability in HIV affects viral eradication. Proc Natl Acad Sci U S A 2014, 111:13251-13252.
45. Ho Y.C., Shan L., Hosmane N., Wang J., Laskey S., Rosenbloom D.I.S., Lai J., Blankson J.N., Siliciano J.D., Siliciano R.F. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 2013, 155:540-551.
46. Mousseau G., Kessing C.F., Fromentin R., Trautmann L., Chomont N., Valente S.T. The Tat inhibitor didehydro-cortistatin A prevents HIV-1 reactivation from latency. MBio 2015, 6:e00465.
47. Dar R.D., Hosmane N.N., Arkin M.R., Siliciano R.F., Weinberger L.S. Screening for noise in gene expression identifies drug synergies. Science 2014, 344:1392-1396.
48. Murphy K. Janeway's Immunobiology 2011, Garland Science. Eighth Edition.
49. Singh A., Weinberger L.S. Stochastic gene expression as a molecular switch for viral latency. Curr Opin Microbiol 2009, 12:460-466.