Are gene loops the cause of transcriptional noise?

Trends in Genetics

Volumn 29, Issue 6, 2013, Pages 333-338

  Hebenstreit, Daniel ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Bursting; Gene loops; Noise; Transcription

Indexed keywords

MESSENGER RNA;

DICTYOSTELIUM; DROSOPHILA; ESCHERICHIA COLI; EUKARYOTE; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENETICS; HUMAN; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; SACCHAROMYCES CEREVISIAE; TATA BOX;

GENE EXPRESSION REGULATION; NUCLEIC ACID CONFORMATION; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 84878203143     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2013.04.001     Document Type: Review

References (80)

1. Balazsi G., et al. Cellular decision making and biological noise: from microbes to mammals. Cell 2011, 144:910-925.
2. Beaumont H.J., et al. Experimental evolution of bet hedging. Nature 2009, 462:90-93.
3. Weinberger L.S., et al. Transient-mediated fate determination in a transcriptional circuit of HIV. Nat. Genet. 2008, 40:466-470.
4. Feinerman O., et al. Variability and robustness in T cell activation from regulated heterogeneity in protein levels. Science 2008, 321:1081-1084.
5. Hebenstreit D., et al. Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells. Curr. Opin. Cell Biol. 2012, 24:350-358.
6. Lestas I., et al. Fundamental limits on the suppression of molecular fluctuations. Nature 2010, 467:174-178.
7. Munsky B., et al. Using gene expression noise to understand gene regulation. Science 2012, 336:183-187.
8. Paulsson J. Models of stochastic gene expression. Phys. Life Rev. 2005, 2:157-175.
9. Pedraza J.M., Paulsson J. Effects of molecular memory and bursting on fluctuations in gene expression. Science 2008, 319:339-343.
10. Newman J.R., et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441:840-846.
11. Peccoud J., Ycart B. Markovian modeling of gene-product synthesis. Theor. Popul. Biol. 1995, 48:222-234.
12. Golding I., et al. Real-time kinetics of gene activity in individual bacteria. Cell 2005, 123:1025-1036.
13. So L.H., et al. General properties of transcriptional time series in Escherichia coli. Nat. Genet. 2011, 43:554-560.
14. Zong C., et al. Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene. Mol. Syst. Biol. 2010, 6:440.
15. Zenklusen D., et al. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat. Struct. Mol. Biol. 2008, 15:1263-1271.
16. Weinberger L., et al. Expression noise and acetylation profiles distinguish HDAC functions. Mol. Cell 2012, 47:193-202.
17. Chubb J.R., et al. Transcriptional pulsing of a developmental gene. Curr. Biol. 2006, 16:1018-1025.
18. Pare A., et al. Visualization of individual Scr mRNAs during Drosophila embryogenesis yields evidence for transcriptional bursting. Curr. Biol. 2009, 19:2037-2042.
19. Hebenstreit D., et al. RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol. Syst. Biol. 2011, 7:497.
20. Singh A., et al. 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.
21. Raj A., et al. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 2006, 4:e309.
22. Suter D.M., et al. Mammalian genes are transcribed with widely different bursting kinetics. Science 2011, 332:472-474.
23. Taniguchi Y., et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010, 329:533-538.
24. Dar R.D., et al. Transcriptional burst frequency and burst size are equally modulated across the human genome. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:17454-17459.
25. Kepler T.B., Elston T.C. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys. J. 2001, 81:3116-3136.
26. To T.L., Maheshri N. Noise can induce bimodality in positive transcriptional feedback loops without bistability. Science 2010, 327:1142-1145.
27. Suter D.M., et al. Origins and consequences of transcriptional discontinuity. Curr. Opin. Cell Biol. 2011, 23:657-662.
28. Skupsky R., et al. HIV promoter integration site primarily modulates transcriptional burst size rather than frequency. PLoS Comput. Biol. 2010, 6:e1000952.
29. Raser J.M., O'Shea E.K. Control of stochasticity in eukaryotic gene expression. Science 2004, 304:1811-1814.
30. Adelman K., Lis J.T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat. Rev. Genet. 2012, 13:720-731.
31. Rajala T., et al. Effects of transcriptional pausing on gene expression dynamics. PLoS Comput. Biol. 2010, 6:e1000704.
32. Reppas N.B., et al. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol. Cell 2006, 24:747-757.
33. Dieci G., Sentenac A. Detours and shortcuts to transcription reinitiation. Trends Biochem. Sci. 2003, 28:202-209.
34. Shandilya J., Roberts S.G. The transcription cycle in eukaryotes: from productive initiation to RNA polymerase II recycling. Biochim. Biophy. Acta 2012, 1819:391-400.
35. Blake W.J., et al. Noise in eukaryotic gene expression. Nature 2003, 422:633-637.
36. Schleif R. DNA looping. Annu. Rev. Biochem. 1992, 61:199-223.
37. Vilar J.M., Saiz L. DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise. Curr. Opin. Genet. Dev. 2005, 15:136-144.
38. de Wit E., de Laat W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 2012, 26:11-24.
39. Hampsey M., et al. Control of eukaryotic gene expression: gene loops and transcriptional memory. Adv. Enzyme Regul. 2011, 51:118-125.
40. Anderson L.M., Yang H. DNA looping can enhance lysogenic CI transcription in phage lambda. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:5827-5832.
41. O'Sullivan J.M., et al. Gene loops juxtapose promoters and terminators in yeast. Nat. Genet. 2004, 36:1014-1018.
42. Ansari A., Hampsey M. A role for the CPF 3'-end processing machinery in RNAP II-dependent gene looping. Genes Dev. 2005, 19:2969-2978.
43. Perkins K.J., et al. Transcription-dependent gene looping of the HIV-1 provirus is dictated by recognition of pre-mRNA processing signals. Mol. Cell 2008, 29:56-68.
44. Yun K., et al. Lymphoid enhancer binding factor 1 regulates transcription through gene looping. J. Immunol. 2009, 183:5129-5137.
45. O'Reilly D., Greaves D.R. Cell-type-specific expression of the human CD68 gene is associated with changes in Pol II phosphorylation and short-range intrachromosomal gene looping. Genomics 2007, 90:407-415.
46. Martin M., et al. Termination factor-mediated DNA loop between termination and initiation sites drives mitochondrial rRNA synthesis. Cell 2005, 123:1227-1240.
47. Hsin J.P., Manley J.L. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev. 2012, 26:2119-2137.
48. Hsin J.P., et al. RNAP II CTD phosphorylated on threonine-4 is required for histone mRNA 3' end processing. Science 2011, 334:683-686.
49. Hintermair C., et al. Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation. EMBO J. 2012, 31:2784-2797.
50. Mayer A., et al. CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science 2012, 336:1723-1725.
51. Glover-Cutter K., et al. TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II. Mol. Cell. Biol. 2009, 29:5455-5464.
52. Singh B.N., Hampsey M. A transcription-independent role for TFIIB in gene looping. Mol. Cell 2007, 27:806-816.
53. Deng W., Roberts S.G. TFIIB and the regulation of transcription by RNA polymerase II. Chromosoma 2007, 116:417-429.
54. Conesa C., Acker J. Sub1/PC4 a chromatin associated protein with multiple functions in transcription. RNA Biol. 2010, 7:287-290.
55. Mapendano C.K., et al. Crosstalk between mRNA 3' end processing and transcription initiation. Mol. Cell 2010, 40:410-422.
56. Grosso A.R., et al. Dynamic transitions in RNA polymerase II density profiles during transcription termination. Genome Res. 2012, 22:1447-1456.
57. Li G., et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 2012, 148:84-98.
58. Brookes E., et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012, 10:157-170.
59. Krishna S., et al. Stochastic simulations of the origins and implications of long-tailed distributions in gene expression. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:4771-4776.
60. Murphy K.F., et al. Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res. 2010, 38:2712-2726.
61. Basehoar A.D., et al. Identification and distinct regulation of yeast TATA box-containing genes. Cell 2004, 116:699-709.
62. Dantonel J.C., et al. Transcription factor TFIID recruits factor CPSF for formation of 3' end of mRNA. Nature 1997, 389:399-402.
63. Laine J.P., et al. A physiological role for gene loops in yeast. Genes Dev. 2009, 23:2604-2609.
64. Peterlin B.M., Price D.H. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 2006, 23:297-305.
65. Glover-Cutter K., et al. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat. Struct. Mol. Biol. 2008, 15:71-78.
66. Wade J.T., Struhl K. The transition from transcriptional initiation to elongation. Curr. Opin. Genet. Dev. 2008, 18:130-136.
67. Tan R.Z., van Oudenaarden A. Transcript counting in single cells reveals dynamics of rDNA transcription. Mol. Syst. Biol. 2010, 6:358.
68. Kempers-Veenstra A.E., et al. 3'-End formation of transcripts from the yeast rRNA operon. EMBO J. 1986, 5:2703-2710.
69. Nemeth A., et al. Epigenetic regulation of TTF-I-mediated promoter-terminator interactions of rRNA genes. EMBO J. 2008, 27:1255-1265.
70. Zhang Z., et al. Negative elongation factor NELF represses human immunodeficiency virus transcription by pausing the RNA polymerase II complex. J. Biol. Chem. 2007, 282:16981-16988.
71. Levens D. How the c-myc promoter works and why it sometimes does not. J. Natl. Cancer Inst. Monogr. 2008, 39:41-43.
72. Liu X., et al. RNA polymerase II transcription: structure and mechanism. Biochim. Biophys. Acta 2013, 1829:2-8.
73. Raj A., et al. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 2008, 5:877-879.
74. Tan-Wong S.M., et al. Gene loops enhance transcriptional directionality. Science 2012, 338:671-675.
75. Henikoff S., Shilatifard A. Histone modification: cause or cog?. Trends Genet. 2011, 27:389-396.
76. Bernstein B.E., et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006, 125:315-326.
77. Min I.M., et al. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev. 2011, 25:742-754.
78. Yadon A.N., et al. DNA looping facilitates targeting of a chromatin remodeling enzyme. Mol. Cell 2013, 50:93-103.
79. Sutherland H., Bickmore W.A. Transcription factories: gene expression in unions?. Nat. Rev. Genet. 2009, 10:457-466.
80. Larkin J.D., et al. Dynamic reconfiguration of long human genes during one transcription cycle. Mol. Cell. Biol. 2012, 32:2738-2747.