Biochemical Genetics

, Volume 45, Issue 1–2, pp 131–137 | Cite as

Relationship Between mRNA Stability and Length: An Old Question with a New Twist

  • Liang Feng
  • Deng-Ke NiuEmail author

The half-life of individual mRNA plays a central role in controlling the level of gene expression. However, the determinants of mRNA stability have not yet been well defined. Most previous studies suggest that mRNA length does not affect its stability. Here, we show significant negative correlations between mRNA length and stability in human and Escherichia coli, but not in Saccharomyces cerevisiae or Bacillus subtilis. This finding suggests the possibility that endonucleolytic attacks by RNA endonuclease and/or mechanical damage may strongly influence mRNA stability in both prokaryotes and eukaryotes.


mRNA half-life mRNA-decay rate mRNA length mRNA degradation 



We would like to thank an anonymous referee for comments, Dr. L. Hederstedt of Lund University for providing the data of B. subtilis mRNA half-lives, Shu-Wei Li for help in parsing mRNA length, and Lei Zhu for discussion. This work was supported by National Natural Science Foundation of China (Grant No. 30270695) and Beijing Normal University.


  1. Bernstein, J. A., Khodursky, A. B., Lin, P. H., Lin-Ghao, S., and Cohen, S. N. (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.PubMedCrossRefGoogle Scholar
  2. Bernstein, J. A., Lin, P. H., Cohen, S. N., and Lin-Chao, S. (2004). Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc. Natl. Acad. Sci. U. S. A. 101:2758–2763.PubMedCrossRefGoogle Scholar
  3. Brown, T. A. (2002) Genomes, 2nd edn. John Wiley & Sons, New York.Google Scholar
  4. Dodson, R. E., and Shapiro, D. J. (2002). Regulation of pathways of mRNA destabilization and stabilization. Prog. Nucleic Acid Res. Mol. Biol. 72:129–164.PubMedGoogle Scholar
  5. Doma, M. K., and Parker, R. (2006). Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440:561–564.PubMedCrossRefGoogle Scholar
  6. Hambraeus, G., von Wachenfeldt, C., and Hederstedt, L. (2003). Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs. Mol. Genet. Genomics 269:706– 714.PubMedCrossRefGoogle Scholar
  7. Herrick, D., Parker, R., and Jacobson, A. (1990). Identification and comparison of stable and unstable messenger-RNAs in Saccharomyces cerevisiae. Mol. Cell. Biol. 10:2269–2284.PubMedGoogle Scholar
  8. Holstege, F. C. P., Jennings, E. G, Wyrick, J. J., Lee, T. I., Hengartner, C. J., Green, M. R., Golub, T. R., Lander, E. S., and Young, R. A. (1998). Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95:717–728.PubMedCrossRefGoogle Scholar
  9. Jain, C. (2002). Degradation of mRNA in Escherichia coli. IUBMB Life 54:315–321.PubMedCrossRefGoogle Scholar
  10. Kang, J. H., Kim, S. A., and Hong, K. J. (2006). Induction of TSPI gene expression by heat shock is mediated via an increase in mRNA stability. FEBS Lett 580:510–516.PubMedCrossRefGoogle Scholar
  11. Khodursky, A. B., and Bernstein, J. A. (2003). Life after transcription: Revisiting the fate of messenger RNA. Trends Genet. 19:113–115.PubMedCrossRefGoogle Scholar
  12. Knapinska, A. M., Irizarry-Barreto, P., Adusumalli, S., Androulakis, L., and Brewer, G. (2005). Molecular mechanisms regulating mRNA stability: Physiological and pathological significance. Curr. Genomics 6:471–486.CrossRefGoogle Scholar
  13. Mata, J., Marguerat, S., and Bahler, A. (2005). Post-transcriptional control of gene expression: A genome-wide perspective. Trends Biochem. Sci. 30:506–514.PubMedCrossRefGoogle Scholar
  14. Meyer, S., Temme, C., and Wahle, E. (2004). Messenger RNA turnover in eukaryotes: Pathways and enzymes. Crit. Rev. Biochem. Mol. Biol. 39:197–216.PubMedCrossRefGoogle Scholar
  15. Parker, R., and Song, H. W. (2004). The enzymes and control of eukaryotic mRNA turnover. Nat. Struct. Mol. Biol. 11:121–127.PubMedCrossRefGoogle Scholar
  16. Patthy, L. (1999). Genome evolution and the evolution of exon-shuffling: A review. Gene 238:103–114.PubMedCrossRefGoogle Scholar
  17. Patthy L. (2003). Modular assembly of genes and the evolution of new functions. Genetica 118:217–231.PubMedCrossRefGoogle Scholar
  18. Raghavan, A., Ogilvie, R. L., Reilly, C., Abelson, M. L., Raghavan, S., Vasdewani, J., Krathwohl, M., and Bohjanen, P. R. (2002). Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res. 30:5529–5538.PubMedCrossRefGoogle Scholar
  19. Santiago, T. C., Purvis, I. J., Bettany, A. J., and Brown, A. J. (1986). The relationship between mRNA stability and length in Saccharomyces cerevisiae. Nucleic Acids Res. 14:8347–8360.PubMedCrossRefGoogle Scholar
  20. Selinger, D. W., Saxena, R. M., Cheung, K. J., Church, G. M., and Rosenow, C. (2003). Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res. 13:216–223.PubMedCrossRefGoogle Scholar
  21. Shapiro, R. A., Herrick, D., Manrow, R. E., Blinder, D., and Jacobson, A. (1988). Determinants of mRNA stability in Diclyostelium discoideum amoebae: differences in poly(A) tail length, ribosome loading, and mRNA size cannot account for the heterogeneity of mRNA decay rates. Mol. Cell. Biol. 8:1957–1969.PubMedGoogle Scholar
  22. Tollervey, D. (2006). RNA lost in translation. Nature 440:425–426.PubMedCrossRefGoogle Scholar
  23. Wang, Y. L., Liu, C. L., Storey, J. D., Tibshirani, R. J., Herschlag, D., and Brown, P. O. (2002). Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. U. S. A. 99:5860–5865.PubMedCrossRefGoogle Scholar
  24. Wilusz, C. J., and Wilusz, J. (2004). Bringing the role of mRNA decay in the control of gene expression into focus. Trends Genet. 20:491–497.PubMedCrossRefGoogle Scholar
  25. Yamashita, A., Chang, T. C., Yamashita, Y., Zhu, W., Zhong, Z., Chen, C. Y., and Shyu, A. B. (2005). Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover. Nat. Struct. Mol. Biol. 12:1054–1063.PubMedCrossRefGoogle Scholar
  26. Yang, E., van Nimwegen, E., Zavolan, M., Rajewsky, N., Schroeder, M., Magnasco, M., and Darnell, J. E. (2003). Decay rates of human mRNAs: Correlation with functional characteristics and sequence attributes. Genome Res. 13:1863–1872.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life SciencesBeijing Normal UniversityBeijingP.R. China

Personalised recommendations