Abstract
Messenger RNA deadenylation is a process that allows rapid regulation of gene expression in response to different cellular conditions. The change of the mRNA poly(A) tail length by the activation of deadenylation might regulate gene expression by affecting mRNA stability, mRNA transport, or translation initiation. Activation of deadenylation processes are highly regulated and associated with different cellular conditions such as cancer, development, mRNA surveillance, DNA damage response, and cell differentiation. In the last few years, new technologies for studying deadenylation have been developed. Here we overview concepts related to deadenylation and its regulation in eukaryotic cells. We also describe some of the most commonly used protocols to study deadenylation in eukaryotic cells.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bentley DL (2005) Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr Opin Cell Biol 17(3):251–256
Sheets MD, Wickens M (1989) Two phases in the addition of a poly(A) tail. Genes Dev 3(9):1401–1412
Wilusz CJ, Gao M, Jones CL et al (2001) Poly(A)-binding proteins regulate both mRNA deadenylation and decapping in yeast cytoplasmic extracts. RNA 7(10):1416–1424
Chen CY, Shyu AB (2003) Rapid deadenylation triggered by a nonsense codon precedes decay of the RNA body in a mammalian cytoplasmic nonsense-mediated decay pathway. Mol Cell Biol 23(14):4805–4813
Parker R, Song H (2004) The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 11(2):121–127
Beelman CA, Parker R (1995) Degradation of mRNA in eukaryotes. Cell 81(2):179–183
Caponigro G, Parker R (1996) mRNA turnover in yeast promoted by the MATalpha1 instability element. Nucleic Acids Res 24(21):4304–4312
Mukherjee D, Gao M, O'Connor JP et al (2002) The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements. EMBO J 21(1–2):165–174
Goldstrohm AC, Wickens M (2008) Multifunctional deadenylase complexes diversify mRNA control. Nat Rev Mol Cell Biol 9(4):337–344
Thore S, Mauxion F, Seraphin B et al (2003) X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex. EMBO Rep 4(12):1150–1155
Zuo Y, Deutscher MP (2001) Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res 29(5):1017–1026
Doidge R, Mittal S, Aslam A et al (2012) The anti-proliferative activity of BTG/TOB proteins is mediated via the Caf1a (CNOT7) and Caf1b (CNOT8) deadenylase subunits of the Ccr4-not complex. PLoS One 7(12):e51331
Lagnado CA, Brown CY, Goodall GJ (1994) AUUUA is not sufficient to promote poly(A) shortening and degradation of an mRNA: the functional sequence within AU-rich elements may be UUAUUUA(U/A)(U/A). Mol Cell Biol 14(12):7984–7995
Chen CY, Shyu AB (1995) AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem Sci 20(11):465–470
Zubiaga AM, Belasco JG, Greenberg ME (1995) The nonamer UUAUUUAUU is the key AU-rich sequence motif that mediates mRNA degradation. Mol Cell Biol 15(4):2219–2230
Ma WJ, Cheng S, Campbell C et al (1996) Cloning and characterization of HuR, a ubiquitously expressed Elav-like protein. J Biol Chem 271(14):8144–8151
Fan XC, Steitz JA (1998) Overexpression of HuR, a nuclear-cytoplasmic shuttling protein, increases the in vivo stability of ARE-containing mRNAs. EMBO J 17(12):3448–3460
Barreau C, Paillard L, Osborne HB (2005) AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res 33(22):7138–7150
Westmark CJ, Bartleson VB, Malter JS (2005) RhoB mRNA is stabilized by HuR after UV light. Oncogene 24(3):502–511
Gherzi R, Lee KY, Briata P et al (2004) A KH domain RNA binding protein, KSRP, promotes ARE-directed mRNA turnover by recruiting the degradation machinery. Mol Cell 14(5):571–583
Moraes KC, Wilusz CJ, Wilusz J (2006) CUG-BP binds to RNA substrates and recruits PARN deadenylase. RNA 12(6):1084–1091
Korner CG, Wahle E (1997) Poly(A) tail shortening by a mammalian poly(A)-specific 3′-exoribonuclease. J Biol Chem 272(16):10448–10456
Lai WS, Kennington EA, Blackshear PJ (2003) Tristetraprolin and its family members can promote the cell-free deadenylation of AU-rich element-containing mRNAs by poly(A) ribonuclease. Mol Cell Biol 23(11):3798–3812
Fabian MR, Mathonnet G, Sundermeier T et al (2009) Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell 35(6):868–880
Johnson SM, Grosshans H, Shingara J et al (2005) RAS is regulated by the let-7 microRNA family. Cell 120(5):635–647
Sampson VB, Rong NH, Han J et al (2007) MicroRNA let-7a down-regulates MYC and reverts MYC-induced growth in Burkitt lymphoma cells. Cancer Res 67(20):9762–9770
Wakiyama M, Takimoto K, Ohara O et al (2007) Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system. Genes Dev 21(15):1857–1862
Robb GB, Brown KM, Khurana J et al (2005) Specific and potent RNAi in the nucleus of human cells. Nat Struct Mol Biol 12(2):133–137
Nishi K, Nishi A, Nagasawa T et al (2013) Human TNRC6A is an Argonaute-navigator protein for microRNA-mediated gene silencing in the nucleus. RNA 19(1):17–35
Doidge R, Mittal S, Aslam A et al (2012) Deadenylation of cytoplasmic mRNA by the mammalian Ccr4-Not complex. Biochem Soc Trans 40(4):896–901
Suzuki A, Saba R, Miyoshi K et al (2012) Interaction between NANOS2 and the CCR4-NOT deadenylation complex is essential for male germ cell development in mouse. PLoS One 7(3):e33558
Van Etten J, Schagat TL, Hrit J et al (2012) Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs. J Biol Chem 287(43):36370–36383
Maragozidis P, Karangeli M, Labrou M et al (2012) Alterations of deadenylase expression in acute leukemias: evidence for poly(a)-specific ribonuclease as a potential biomarker. Acta Haematol 128(1):39–46
Martinez J, Ren YG, Nilsson P et al (2001) The mRNA cap structure stimulates rate of poly(A) removal and amplifies processivity of degradation. J Biol Chem 276(30):27923–27929
Dehlin E, Wormington M, Korner CG, Wahle E (2000) Cap-dependent deadenylation of mRNA. EMBO J 19(5):1079–1086
Balatsos NA, Nilsson P, Mazza C et al (2006) Inhibition of mRNA deadenylation by the nuclear cap binding complex (CBC). J Biol Chem 281(7):4517–4522
Cevher MA, Zhang X, Fernandez S et al (2010) Nuclear deadenylation/polyadenylation factors regulate 3′ processing in response to DNA damage. EMBO J 29(10):1674–1687
Lehner B, Sanderson CM (2004) A protein interaction framework for human mRNA degradation. Genome Res 14(7):1315–1323
Devany E, Zhang X, Park JY et al (2013) Positive and negative feedback loops in the p53 and mRNA 3′ processing pathways. Proc Natl Acad Sci U S A 110(9):3351–3356
Udagawa T, Swanger SA, Takeuchi K et al (2012) Bidirectional control of mRNA translation and synaptic plasticity by the cytoplasmic polyadenylation complex. Mol Cell 47(2):253–266
Azzouz N, Panasenko OO, Colau G et al (2009) The CCR4-NOT complex physically and functionally interacts with TRAMP and the nuclear exosome. PLoS One 4(8):e6760
Lee JE, Lee JY, Trembly J et al (2012) The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts. PLoS Genet 8(8):e1002901
Meijer HA, Bushell M, Hill K et al (2007) A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 35(19):e132
Astrom J, Astrom A, Virtanen A (1991) In vitro deadenylation of mammalian mRNA by a HeLa cell 3′ exonuclease. EMBO J 10(10):3067–3071
Lowell JE, Rudner DZ, Sachs AB (1992) 3′-UTR-dependent deadenylation by the yeast poly(A) nuclease. Genes Dev 6(11):2088–2099
Sachs AB, Deardorff JA (1992) Translation initiation requires the PAB-dependent poly(A) ribonuclease in yeast. Cell 70(6):961–973
Garneau NL, Wilusz CJ, Wilusz J (2008) Chapter 5. In vivo analysis of the decay of transcripts generated by cytoplasmic RNA viruses. Methods Enzymol 449:97–123
Mittal S, Aslam A, Doidge R et al (2011) The Ccr4a (CNOT6) and Ccr4b (CNOT6L) deadenylase subunits of the human Ccr4-Not complex contribute to the prevention of cell death and senescence. Mol Biol Cell 22(6):748–758
Piao X, Zhang X, Wu L et al (2010) CCR4-NOT deadenylates mRNA associated with RNA-induced silencing complexes in human cells. Mol Cell Biol 30(6):1486–1494
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this protocol
Cite this protocol
Zhang, X., Kleiman, F.E., Devany, E. (2014). Deadenylation and Its Regulation in Eukaryotic Cells. In: Rorbach, J., Bobrowicz, A. (eds) Polyadenylation. Methods in Molecular Biology, vol 1125. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-971-0_23
Download citation
DOI: https://doi.org/10.1007/978-1-62703-971-0_23
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-970-3
Online ISBN: 978-1-62703-971-0
eBook Packages: Springer Protocols