Skip to main content
PMC home page
RNA logoLink to RNA
. 2001 Jul;7(7):1034–1042. doi: 10.1017/s1355838201010329

Position and sequence requirements for poly(A) length regulation by the poly(A) limiting element.

J D Gupta 1, H Gu 1, D R Schoenberg 1
PMCID: PMC1370144  PMID: 11453064

Abstract

The poly(A)-limiting element (PLE) is a cis-acting sequence that acts to limit poly(A) tail length on pre-mRNA to <20 nt. Functional PLEs are present in a number of genes, underscoring the generality of this control mechanism. The current study sought to define further the position requirements for poly(A) length regulation and the core sequence that comprises a PLE. Increasing the spacing between the PLE and the upstream 3' splice site or between the PLE and the downstream AAUAAA had no effect on poly(A) length control. However, moving the PLE from the terminal exon to either an upstream exon or intron eliminated poly(A) length control. Poly(A) length control was further evaluated using a battery of constructs in which the PLE was maintained in the terminal exon, but where upstream introns were either deleted, modified, or replaced with a polypyrimidine tract. Poly(A) length control was retained in all cases, indicating that the key feature is the presence of the PLE in the terminal exon. A battery of mutations demonstrated the importance of the 5' pyrimidine-rich portion of the element. Finally, UV crosslinking experiments identified an approximately 62-kDa protein in Hela nuclear extract that binds to a wild-type 23-nt PLE RNA oligonucleotides but not to a mutated nonfunctional form of the element.

Full Text

The Full Text of this article is available as a PDF (178.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Antoniou M., Geraghty F., Hurst J., Grosveld F. Efficient 3'-end formation of human beta-globin mRNA in vivo requires sequences within the last intron but occurs independently of the splicing reaction. Nucleic Acids Res. 1998 Feb 1;26(3):721–729. doi: 10.1093/nar/26.3.721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Audic Y., Omilli F., Osborne H. B. Embryo deadenylation element-dependent deadenylation is enhanced by a cis element containing AUU repeats. Mol Cell Biol. 1998 Dec;18(12):6879–6884. doi: 10.1128/mcb.18.12.6879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baurén G., Wieslander L. Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell. 1994 Jan 14;76(1):183–192. doi: 10.1016/0092-8674(94)90182-1. [DOI] [PubMed] [Google Scholar]
  4. Berget S. M. Exon recognition in vertebrate splicing. J Biol Chem. 1995 Feb 10;270(6):2411–2414. doi: 10.1074/jbc.270.6.2411. [DOI] [PubMed] [Google Scholar]
  5. Chen Z., Li Y., Krug R. M. Influenza A virus NS1 protein targets poly(A)-binding protein II of the cellular 3'-end processing machinery. EMBO J. 1999 Apr 15;18(8):2273–2283. doi: 10.1093/emboj/18.8.2273. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cooke C., Hans H., Alwine J. C. Utilization of splicing elements and polyadenylation signal elements in the coupling of polyadenylation and last-intron removal. Mol Cell Biol. 1999 Jul;19(7):4971–4979. doi: 10.1128/mcb.19.7.4971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Custódio N., Carmo-Fonseca M., Geraghty F., Pereira H. S., Grosveld F., Antoniou M. Inefficient processing impairs release of RNA from the site of transcription. EMBO J. 1999 May 17;18(10):2855–2866. doi: 10.1093/emboj/18.10.2855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Das Gupta J., Gu H., Chernokalskaya E., Gao X., Schoenberg D. R. Identification of two cis-acting elements that independently regulate the length of poly(A) on Xenopus albumin pre-mRNA. RNA. 1998 Jul;4(7):766–776. doi: 10.1017/s1355838298971837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gilmartin G. M., Fleming E. S., Oetjen J., Graveley B. R. CPSF recognition of an HIV-1 mRNA 3'-processing enhancer: multiple sequence contacts involved in poly(A) site definition. Genes Dev. 1995 Jan 1;9(1):72–83. doi: 10.1101/gad.9.1.72. [DOI] [PubMed] [Google Scholar]
  10. Gu H., Das Gupta J., Schoenberg D. R. The poly(A)-limiting element is a conserved cis-acting sequence that regulates poly(A) tail length on nuclear pre-mRNAs. Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):8943–8948. doi: 10.1073/pnas.96.16.8943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gunderson S. I., Beyer K., Martin G., Keller W., Boelens W. C., Mattaj L. W. The human U1A snRNP protein regulates polyadenylation via a direct interaction with poly(A) polymerase. Cell. 1994 Feb 11;76(3):531–541. doi: 10.1016/0092-8674(94)90116-3. [DOI] [PubMed] [Google Scholar]
  12. Gunderson S. I., Polycarpou-Schwarz M., Mattaj I. W. U1 snRNP inhibits pre-mRNA polyadenylation through a direct interaction between U1 70K and poly(A) polymerase. Mol Cell. 1998 Jan;1(2):255–264. doi: 10.1016/s1097-2765(00)80026-x. [DOI] [PubMed] [Google Scholar]
  13. Gunderson S. I., Vagner S., Polycarpou-Schwarz M., Mattaj I. W. Involvement of the carboxyl terminus of vertebrate poly(A) polymerase in U1A autoregulation and in the coupling of splicing and polyadenylation. Genes Dev. 1997 Mar 15;11(6):761–773. doi: 10.1101/gad.11.6.761. [DOI] [PubMed] [Google Scholar]
  14. Levitt N., Briggs D., Gil A., Proudfoot N. J. Definition of an efficient synthetic poly(A) site. Genes Dev. 1989 Jul;3(7):1019–1025. doi: 10.1101/gad.3.7.1019. [DOI] [PubMed] [Google Scholar]
  15. Lou H., Gagel R. F., Berget S. M. An intron enhancer recognized by splicing factors activates polyadenylation. Genes Dev. 1996 Jan 15;10(2):208–219. doi: 10.1101/gad.10.2.208. [DOI] [PubMed] [Google Scholar]
  16. Lou H., Helfman D. M., Gagel R. F., Berget S. M. Polypyrimidine tract-binding protein positively regulates inclusion of an alternative 3'-terminal exon. Mol Cell Biol. 1999 Jan;19(1):78–85. doi: 10.1128/mcb.19.1.78. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Moreira A., Takagaki Y., Brackenridge S., Wollerton M., Manley J. L., Proudfoot N. J. The upstream sequence element of the C2 complement poly(A) signal activates mRNA 3' end formation by two distinct mechanisms. Genes Dev. 1998 Aug 15;12(16):2522–2534. doi: 10.1101/gad.12.16.2522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Paillard L., Omilli F., Legagneux V., Bassez T., Maniey D., Osborne H. B. EDEN and EDEN-BP, a cis element and an associated factor that mediate sequence-specific mRNA deadenylation in Xenopus embryos. EMBO J. 1998 Jan 2;17(1):278–287. doi: 10.1093/emboj/17.1.278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Pastori R. L., Moskaitis J. E., Buzek S. W., Schoenberg D. R. Coordinate estrogen-regulated instability of serum protein-coding messenger RNAs in Xenopus laevis. Mol Endocrinol. 1991 Apr;5(4):461–468. doi: 10.1210/mend-5-4-461. [DOI] [PubMed] [Google Scholar]
  20. Rao M. N., Chernokalskaya E., Schoenberg D. R. Regulated nuclear polyadenylation of Xenopus albumin pre-mRNA. Nucleic Acids Res. 1996 Oct 15;24(20):4078–4083. doi: 10.1093/nar/24.20.4078. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Richter J. D. Cytoplasmic polyadenylation in development and beyond. Microbiol Mol Biol Rev. 1999 Jun;63(2):446–456. doi: 10.1128/mmbr.63.2.446-456.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Rüegsegger U., Beyer K., Keller W. Purification and characterization of human cleavage factor Im involved in the 3' end processing of messenger RNA precursors. J Biol Chem. 1996 Mar 15;271(11):6107–6113. doi: 10.1074/jbc.271.11.6107. [DOI] [PubMed] [Google Scholar]
  23. Sallés F. J., Richards W. G., Strickland S. Assaying the polyadenylation state of mRNAs. Methods. 1999 Jan;17(1):38–45. doi: 10.1006/meth.1998.0705. [DOI] [PubMed] [Google Scholar]
  24. Schek N., Cooke C., Alwine J. C. Definition of the upstream efficiency element of the simian virus 40 late polyadenylation signal by using in vitro analyses. Mol Cell Biol. 1992 Dec;12(12):5386–5393. doi: 10.1128/mcb.12.12.5386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Schoenberg D. R., Moskaitis J. E., Smith L. H., Jr, Pastori R. L. Extranuclear estrogen-regulated destabilization of Xenopus laevis serum albumin mRNA. Mol Endocrinol. 1989 May;3(5):805–814. doi: 10.1210/mend-3-5-805. [DOI] [PubMed] [Google Scholar]
  26. Sittler A., Gallinaro H., Jacob M. The secondary structure of the adenovirus-2 L4 polyadenylation domain: evidence for a hairpin structure exposing the AAUAAA signal in its loop. J Mol Biol. 1995 May 5;248(3):525–540. doi: 10.1006/jmbi.1995.0240. [DOI] [PubMed] [Google Scholar]
  27. Vagner S., Vagner C., Mattaj I. W. The carboxyl terminus of vertebrate poly(A) polymerase interacts with U2AF 65 to couple 3'-end processing and splicing. Genes Dev. 2000 Feb 15;14(4):403–413. [PMC free article] [PubMed] [Google Scholar]
  28. Wu L., Good P. J., Richter J. D. The 36-kilodalton embryonic-type cytoplasmic polyadenylation element-binding protein in Xenopus laevis is ElrA, a member of the ELAV family of RNA-binding proteins. Mol Cell Biol. 1997 Nov;17(11):6402–6409. doi: 10.1128/mcb.17.11.6402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Zhao J., Hyman L., Moore C. Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev. 1999 Jun;63(2):405–445. doi: 10.1128/mmbr.63.2.405-445.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES