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. 1986 Apr 25;14(8):3557–3571. doi: 10.1093/nar/14.8.3557

Sequence signals which may be required for efficient formation of mRNA 3' termini.

R Nussinov
PMCID: PMC339793  PMID: 3754635

Abstract

It has been known for sometime that AATAAA (Proudfoot and Brownlee, 1976) is often required for 3' mRNA processing. More recently, McLauchlan et al. (1985) have shown the high incidence of YGTGTTYY (Y is a pyrimidine) downstream from the poly (A) addition site. Our results fully support their findings. There have been indications that additional sequences are required either for transcription termination of mRNA or for its cleavage/processing. Here I present the results of detailed analysis of mammalian DNA sequences around the 3' ends of mRNAs. The distributions of 256 quartets and some pentamers have been studied. Except for the AATAAA several additional signals emerge, namely, the homooligomers A4-5, T4-5 and C4-5, C3-4 interspersed with a single T, alternations of T and G, TTCTT and GGAGG. These are highly regular sequences which may exhibit unique conformations. The results also show a clear-cut asymmetry in the distribution of complementary oligomers on the same DNA strand. The possibility that at least some of these signals are recognized on the DNA and thus play a role in the termination process is discussed.

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Selected References

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

  1. Arnott S., Chandrasekaran R., Hall I. H., Puigjaner L. C., Walker J. K., Wang M. DNA secondary structures: helices, wrinkles, and junctions. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):53–65. doi: 10.1101/sqb.1983.047.01.008. [DOI] [PubMed] [Google Scholar]
  2. Birchmeier C., Grosschedl R., Birnstiel M. L. Generation of authentic 3' termini of an H2A mRNA in vivo is dependent on a short inverted DNA repeat and on spacer sequences. Cell. 1982 Apr;28(4):739–745. doi: 10.1016/0092-8674(82)90053-8. [DOI] [PubMed] [Google Scholar]
  3. Birnstiel M. L., Busslinger M., Strub K. Transcription termination and 3' processing: the end is in site! Cell. 1985 Jun;41(2):349–359. doi: 10.1016/s0092-8674(85)80007-6. [DOI] [PubMed] [Google Scholar]
  4. Cheung S., Arndt K., Lu P. Correlation of lac operator DNA imino proton exchange kinetics with its function. Proc Natl Acad Sci U S A. 1984 Jun;81(12):3665–3669. doi: 10.1073/pnas.81.12.3665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Collins F. S., Metherall J. E., Yamakawa M., Pan J., Weissman S. M., Forget B. G. A point mutation in the A gamma-globin gene promoter in Greek hereditary persistence of fetal haemoglobin. Nature. 1985 Jan 24;313(6000):325–326. doi: 10.1038/313325a0. [DOI] [PubMed] [Google Scholar]
  6. Desiderio S., Baltimore D. Double-stranded cleavage by cell extracts near recombinational signal sequences of immunoglobulin genes. 1984 Apr 26-May 2Nature. 308(5962):860–862. doi: 10.1038/308860a0. [DOI] [PubMed] [Google Scholar]
  7. Dierks P., van Ooyen A., Cochran M. D., Dobkin C., Reiser J., Weissmann C. Three regions upstream from the cap site are required for efficient and accurate transcription of the rabbit beta-globin gene in mouse 3T6 cells. Cell. 1983 Mar;32(3):695–706. doi: 10.1016/0092-8674(83)90055-7. [DOI] [PubMed] [Google Scholar]
  8. Drew H. R., Travers A. A. DNA structural variations in the E. coli tyrT promoter. Cell. 1984 Jun;37(2):491–502. doi: 10.1016/0092-8674(84)90379-9. [DOI] [PubMed] [Google Scholar]
  9. Fitzgerald M., Shenk T. The sequence 5'-AAUAAA-3'forms parts of the recognition site for polyadenylation of late SV40 mRNAs. Cell. 1981 Apr;24(1):251–260. doi: 10.1016/0092-8674(81)90521-3. [DOI] [PubMed] [Google Scholar]
  10. Gelinas R., Endlich B., Pfeiffer C., Yagi M., Stamatoyannopoulos G. G to A substitution in the distal CCAAT box of the A gamma-globin gene in Greek hereditary persistence of fetal haemoglobin. Nature. 1985 Jan 24;313(6000):323–325. doi: 10.1038/313323a0. [DOI] [PubMed] [Google Scholar]
  11. Hinnebusch A. G., Fink G. R. Repeated DNA sequences upstream from HIS1 also occur at several other co-regulated genes in Saccharomyces cerevisiae. J Biol Chem. 1983 Apr 25;258(8):5238–5247. [PubMed] [Google Scholar]
  12. Irani M. H., Orosz L., Adhya S. A control element within a structural gene: the gal operon of Escherichia coli. Cell. 1983 Mar;32(3):783–788. doi: 10.1016/0092-8674(83)90064-8. [DOI] [PubMed] [Google Scholar]
  13. Karin M., Haslinger A., Holtgreve H., Richards R. I., Krauter P., Westphal H. M., Beato M. Characterization of DNA sequences through which cadmium and glucocorticoid hormones induce human metallothionein-IIA gene. Nature. 1984 Apr 5;308(5959):513–519. doi: 10.1038/308513a0. [DOI] [PubMed] [Google Scholar]
  14. Krieg P. A., Melton D. A. Formation of the 3' end of histone mRNA by post-transcriptional processing. Nature. 1984 Mar 8;308(5955):203–206. doi: 10.1038/308203a0. [DOI] [PubMed] [Google Scholar]
  15. Langridge R. Nucleic acids and polynucleotides. J Cell Physiol. 1969 Oct;74(2 Suppl):1–20. doi: 10.1002/jcp.1040740403. [DOI] [PubMed] [Google Scholar]
  16. Lennon G. G., Nussinov R. Homonyms, synonyms and mutations of the sequence/structure vocabulary. J Mol Biol. 1984 May 25;175(3):425–430. doi: 10.1016/0022-2836(84)90359-0. [DOI] [PubMed] [Google Scholar]
  17. Levitt M. How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations. Proc Natl Acad Sci U S A. 1978 Feb;75(2):640–644. doi: 10.1073/pnas.75.2.640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lomonossoff G. P., Butler P. J., Klug A. Sequence-dependent variation in the conformation of DNA. J Mol Biol. 1981 Jul 15;149(4):745–760. doi: 10.1016/0022-2836(81)90356-9. [DOI] [PubMed] [Google Scholar]
  19. Lu P., Cheung S., Arndt K. Possible molecular detent in the DNA structure at regulatory sequences. J Biomol Struct Dyn. 1983 Oct;1(2):509–521. doi: 10.1080/07391102.1983.10507458. [DOI] [PubMed] [Google Scholar]
  20. McCall M., Brown T., Kennard O. The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG).poly(dC). J Mol Biol. 1985 Jun 5;183(3):385–396. doi: 10.1016/0022-2836(85)90009-9. [DOI] [PubMed] [Google Scholar]
  21. McDevitt M. A., Imperiale M. J., Ali H., Nevins J. R. Requirement of a downstream sequence for generation of a poly(A) addition site. Cell. 1984 Jul;37(3):993–999. doi: 10.1016/0092-8674(84)90433-1. [DOI] [PubMed] [Google Scholar]
  22. McLauchlan J., Gaffney D., Whitton J. L., Clements J. B. The consensus sequence YGTGTTYY located downstream from the AATAAA signal is required for efficient formation of mRNA 3' termini. Nucleic Acids Res. 1985 Feb 25;13(4):1347–1368. doi: 10.1093/nar/13.4.1347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Nickol J. M., Felsenfeld G. DNA conformation at the 5' end of the chicken adult beta-globin gene. Cell. 1983 Dec;35(2 Pt 1):467–477. doi: 10.1016/0092-8674(83)90180-0. [DOI] [PubMed] [Google Scholar]
  24. Nussinov R. Promoter helical structure variation at the Escherichia coli polymerase interaction sites. J Biol Chem. 1984 Jun 10;259(11):6798–6805. [PubMed] [Google Scholar]
  25. Payvar F., DeFranco D., Firestone G. L., Edgar B., Wrange O., Okret S., Gustafsson J. A., Yamamoto K. R. Sequence-specific binding of glucocorticoid receptor to MTV DNA at sites within and upstream of the transcribed region. Cell. 1983 Dec;35(2 Pt 1):381–392. doi: 10.1016/0092-8674(83)90171-x. [DOI] [PubMed] [Google Scholar]
  26. Proudfoot N. J., Brownlee G. G. 3' non-coding region sequences in eukaryotic messenger RNA. Nature. 1976 Sep 16;263(5574):211–214. doi: 10.1038/263211a0. [DOI] [PubMed] [Google Scholar]
  27. Salditt-Georgieff M., Darnell J. E., Jr A precise termination site in the mouse beta major-globin transcription unit. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4694–4698. doi: 10.1073/pnas.80.15.4694. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  28. Waterman M. S., Arratia R., Galas D. J. Pattern recognition in several sequences: consensus and alignment. Bull Math Biol. 1984;46(4):515–527. doi: 10.1007/BF02459500. [DOI] [PubMed] [Google Scholar]
  29. Weiher H., König M., Gruss P. Multiple point mutations affecting the simian virus 40 enhancer. Science. 1983 Feb 11;219(4585):626–631. doi: 10.1126/science.6297005. [DOI] [PubMed] [Google Scholar]
  30. de Crombrugghe B., Busby S., Buc H. Cyclic AMP receptor protein: role in transcription activation. Science. 1984 May 25;224(4651):831–838. doi: 10.1126/science.6372090. [DOI] [PubMed] [Google Scholar]

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