Complex Degradation Processes Lead to Non-Exponential Decay Patterns and Age-Dependent Decay Rates of Messenger RNA

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Deneke, Carlus ^a,b   Lipowsky, Reinhard ^a   Valleriani, Angelo ^a  

^a MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

^b ROBERT KOCH INSTITUTE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

AGING; ARTICLE; LIFESPAN; MATHEMATICS; MOLECULAR DYNAMICS; PROBABILITY; RNA DEGRADATION; SACCHAROMYCES CEREVISIAE; STATISTICAL MODEL;

HYDROLYSIS; MARKOV CHAINS; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; STOCHASTIC PROCESSES;

EID: 84873620982     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0055442     Document Type: Article

References (44)

1. Lu P, Vogel C, Wang R, Yao X, Marcotte E, (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nature Biotechnology 25: 117-124.
2. Vogel C, de Sousa Abreu R, Ko D, Le S, Shapiro B, et al. (2010) Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Molecular Systems Biology 6: 400.
3. Vogel C, Marcotte E, (2012) Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nature Review Genetics 13: 227-232.
4. Pai AA, Cain CE, Mizrahi-Man O, De Leon S, Lewellen N, et al. (2012) The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels. PLoS Genet 8: e1003000.
5. Belasco JG, (2010) All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat Rev Mol Cell Biol 11: 467-478.
6. Kushner SR, (2002) mRNA decay in Escherichia coli comes of age. J Bacteriol 184: 4658-4665.
7. Deutscher MP, (2006) Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Nucleic Acids Res 34: 659-666.
8. Chen K, Rajewsky N, (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 8: 93-103.
9. Chen CYA, Zheng DH, Xia ZF, Shyu AB, (2009) Ago-TNRC6 triggers microRNA-mediated decay by promoting two deadenylation steps. Nat Struct Mol Biol 16: 1160-U6.
10. Braun JE, Huntzinger E, Fauser M, Izaurralde E, (2011) GW182 Proteins Directly Recruit Cytoplasmic Deadenylase Complexes to miRNA Targets. Mol Cell 44: 120-133.
11. Huntzinger E, Izaurralde E, (2011) Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 12: 99-110.
12. Elgart V, Jia T, Kulkarni R, (2010) Quantifying mRNA Synthesis and Decay Rates Using Small RNAs. Biophys J 98: 2780-2784.
13. Levine E, McHale P, Levine H, (2007) Small regulatory RNAs may sharpen spatial expression patterns. PLoS Comput Biol 3: 2356-2365.
14. Hu WQ, Sweet TJ, Chamnongpol S, Baker KE, Coller J, (2009) Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 461: 225-U96.
15. Even S, Pellegrini O, Zig L, Labas V, Vinh J, et al. (2005) Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E. Nucleic Acids Res. 33: 2141-2152.
16. Condon C, (2010) What is the role of RNase J in mRNA turnover? RNA Biol 7: 316-321.
17. Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN, (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99: 9697-9702.
18. Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C, (2003) Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res 13: 216-223.
19. Steglich C, Lindell D, Futschik M, Rector T, Steen R, et al. (2010) Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus. Genome Biology 11: R54.
20. Andersson AF, Lundgren M, Eriksson S, Rosenlund M, Bernander R, et al. (2006) Global analysis of mRNA stability in the archaeon Sulfolobus. Genome Biology 7: R99.
21. Taniguchi Y, Choi PJ, Li GW, Chen HY, Babu M, et al. (2010) Quantifying E-coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells. Science 329: 533-538.
22. Wang YL, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, et al. (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A 99: 5860-5865.
23. Shalem O, Dahan O, Levo M, Martinez MR, Furman I, et al. (2008) Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Molecular Systems Biology 4: 223.
24. Dolken L, Ruzsics Z, Radle B, Friedel CC, Zimmer R, et al. (2008) High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. Rna-a Publication of the Rna Society 14: 1959-1972.
25. Miller C, Schwalb B, Maier K, Schulz D, Dumcke S, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Molecular Systems Biology 7: 458.
26. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, et al. (2011) Global quantification of mammalian gene expression control. Nature 473: 337-342.
27. Taylor HM, Karlin S (1998) An introduction to stochastic modeling. San Diego: Academic Press, 3rd edition.
28. Liou JJ, Srienc F, Fredrickson AG, (1997) Solutions of population balance models based on a successive generations approach. Chem Eng Sci 52: 1529-1540.
29. Rading MM, Engel TA, Lipowsky R, Valleriani A, (2011) Stationary Size Distributions of Growing Cells with Binary and Multiple Cell Division. Journal of Statistical Physics 145: 1-22.
30. Schmid M, Jensen TH, (2008) Quality control of mRNP in the nucleus. Chromosoma 117: 419-429.
31. Hoyle NP, Castelli LM, Campbell SG, Holmes LE, Ashe MP, (2007) Stress-dependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies. The Journal of Cell Biology 179: 65-74.
32. Zimmer SL, McEvoy SM, Menon S, Read LK, (2012) Additive and Transcript-Specific Effects of KPAP1 and TbRND Activities on 3 Non-Encoded Tail Characteristics and mRNA Stability in Trypanosoma brucei. PLoS ONE 7: e37639.
33. Valleriani A, Ignatova Z, Nagar A, Lipowsky R, (2010) Turnover of messenger RNA: Polysome statistics beyond the steady state. Epl 89: 58003.
34. Nagar A, Valleriani A, Lipowsky R, (2011) Translation by ribosomes with mRNA degradation: Exclusion processes on aging tracks. J Stat Phys 145: 1385-1404.
35. Valleriani A, Zhang G, Nagar A, Ignatova Z, Lipowsky R, (2011) Length-dependent translation of messenger RNA by ribosomes. Physical Review E 83: 042903.
36. Kepes A, (1963) Kinetics of Induced Enzyme Synthesis. Determination of the Mean Life of Galactosidase-Specific Messenger Rna. Biochim Biophys Acta 76: 293-309.
37. Petersen C, (1987) The functional stability of the lacZ transcript is sensitive towards sequence alterations immediately downstream of the ribosome binding site. Mol Gen Genet 209: 179-87.
38. Trcek T, Larson DR, Moldon A, Query CC, Singer RH, (2011) Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast. Cell 147: 1484-97.
39. Xie SN, (2001) Single-molecule approach to enzymology. Single Molecules 2: 229-236.
40. Valleriani A, Liepelt S, Lipowsky R, (2008) Dwell time distributions for kinesin's mechanical steps. Epl 82: 28011.
41. Keller P, Valleriani A, (2012) Single-molecule stochastic times in a reversible bimolecular reaction. J Chem Phys 137: 084106.
42. Berger F, Keller C, Klumpp S, Lipowsky R, (2012) Distinct Transport Regimes for Two Elastically Coupled Molecular Motors. Phys Rev Lett 108: 208101.
43. Thattai M, van Oudenaarden A, (2001) Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci U S A 98: 8614-9.
44. Deneke C, Rudorf S, Valleriani A, (2012) Transient phenomena in gene expression after induction of transcription. PLoS ONE 7: e35044.