Nucleic Acids Research, 2003, Vol. 31, No. 5 1375-1386
© 2003 Oxford University Press
Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures
Molecular Biophysics Department, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, vul. Zabolotnoho, Kyiv, 03143, Ukraine
*To whom correspondence should be addressed. Tel: +380 44 2661109; Fax: +380 44 2660759; Email: dhovorun{at}imbg.org.ua
Primary, secondary and higher-order structures of downstream elements of mammalian pre-mRNA polyadenylation signals [poly(A) signals] are re viewed. We have carried out a detailed analysis on our database of 244 human pre-mRNA poly(A) signals in order to characterize elements in their downstream regions. We suggest that the downstream region of the mammalian pre-mRNA poly(A) signal consists of various simple elements located at different distances from each other. Thus, the downstream region is not described by any precise consensus. Searching our database, we found that 
80% of pre-mRNAs with the AAUAAA or AUUAAA core upstream elements contain simple downstream elements, consisting of U-rich and/or 2GU/U tracts, the former occurring 2-fold more often than the latter. Approximately one-third of the pre-mRNAs analyzed here contain sequences that may form G-quadruplexes. A substantial number of these sequences are located immediately downstream of the poly(A) signal. A possible role of G-rich sequences in the polyadenylation process is discussed. A model of the secondary structure of the SV40 late pre-mRNA poly(A) signal downstream region is presented.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  O. R. Borodulina and D. A. Kramerov Transcripts synthesized by RNA polymerase III can be polyadenylated in an AAUAAA-dependent manner RNA, September 1, 2008; 14(9): 1865 - 1873. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Kikin, Z. Zappala, L. D'Antonio, and P. S. Bagga GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs Nucleic Acids Res., January 11, 2008; 36(suppl_1): D141 - D148. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Patel, A. T. Phan, and V. Kuryavyi Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics Nucleic Acids Res., December 3, 2007; 35(22): 7429 - 7455. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. C. Coutinho, R. R. D. Coletta, E. M. F. Costa, P. R. Pachi, M. C. S. Boguszewski, D. Damiani, B. B. Mendonca, I. J. P. Arnhold, and A. A. L. Jorge Polymorphisms Identified in the Upstream Core Polyadenylation Signal of IGF1 Gene Exon 6 Do Not Cause Pre- and Postnatal Growth Impairment J. Clin. Endocrinol. Metab., December 1, 2007; 92(12): 4889 - 4892. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Dalziel, N. M. Nunes, and A. Furger Two G-Rich Regulatory Elements Located Adjacent to and 440 Nucleotides Downstream of the Core Poly(A) Site of the Intronless Melanocortin Receptor 1 Gene Are Critical for Efficient 3' End Processing Mol. Cell. Biol., March 1, 2007; 27(5): 1568 - 1580. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Liu, J. M. Brockman, B. Dass, L. N. Hutchins, P. Singh, J. R. McCarrey, C. C. MacDonald, and J. H. Graber Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis Nucleic Acids Res., January 12, 2007; 35(1): 234 - 246. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Cheng, R. M. Miura, and B. Tian Prediction of mRNA polyadenylation sites by support vector machine Bioinformatics, October 1, 2006; 22(19): 2320 - 2325. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Dominguez and F. H.-T. Allain NMR structure of the three quasi RNA recognition motifs (qRRMs) of human hnRNP F and interaction studies with Bcl-x G-tract RNA: a novel mode of RNA recognition Nucleic Acids Res., August 2, 2006; 34(13): 3634 - 3645. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Kikin, L. D'Antonio, and P. S Bagga QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W676 - W682. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Kostadinov, N. Malhotra, M. Viotti, R. Shine, L. D'Antonio, and P. Bagga GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences Nucleic Acids Res., January 1, 2006; 34(suppl_1): D119 - D124. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Rommens, O. Bougri, H. Yan, J. M. Humara, J. Owen, K. Swords, and J. Ye Plant-Derived Transfer DNAs Plant Physiology, November 1, 2005; 139(3): 1338 - 1349. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. HU, C. S. LUTZ, J. WILUSZ, and B. TIAN Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation RNA, October 1, 2005; 11(10): 1485 - 1493. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Bego, J. Maciejewski, S. Khaiboullina, G. Pari, and S. St. Jeor Characterization of an Antisense Transcript Spanning the UL81-82 Locus of Human Cytomegalovirus J. Virol., September 1, 2005; 79(17): 11022 - 11034. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. C. Viertlboeck, F. A. Habermann, R. Schmitt, M. A. M. Groenen, L. Du Pasquier, and T. W. Gobel The Chicken Leukocyte Receptor Complex: A Highly Diverse Multigene Family Encoding at Least Six Structurally Distinct Receptor Types J. Immunol., July 1, 2005; 175(1): 385 - 393. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Loke, E. A. Stahlberg, D. G. Strenski, B. J. Haas, P. C. Wood, and Q. Q. Li Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures Plant Physiology, July 1, 2005; 138(3): 1457 - 1468. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Sachchithananthan, S. J. Stasinopoulos, J. Wilusz, and R. L. Medcalf The relationship between the prothrombin upstream sequence element and the G20210A polymorphism: the influence of a competitive environment for mRNA 3'-end formation Nucleic Acids Res., February 17, 2005; 33(3): 1010 - 1020. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Dominski, X.-c. Yang, M. Purdy, E. J. Wagner, and W. F. Marzluff A CPSF-73 Homologue Is Required for Cell Cycle Progression but Not Cell Growth and Interacts with a Protein Having Features of CPSF-100 Mol. Cell. Biol., February 15, 2005; 25(4): 1489 - 1500. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Tian, J. Hu, H. Zhang, and C. S. Lutz A large-scale analysis of mRNA polyadenylation of human and mouse genes Nucleic Acids Res., January 12, 2005; 33(1): 201 - 212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Zhang, J. Hu, M. Recce, and B. Tian PolyA_DB: a database for mammalian mRNA polyadenylation Nucleic Acids Res., January 1, 2005; 33(suppl_1): D116 - D120. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Loewendorf, C. Kruger, E. M. Borst, M. Wagner, U. Just, and M. Messerle Identification of a Mouse Cytomegalovirus Gene Selectively Targeting CD86 Expression on Antigen-Presenting Cells J. Virol., December 1, 2004; 78(23): 13062 - 13071. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Bienvenu, D. Seurin, P. Grellier, P. Froment, M. Baudrimont, P. Monget, Y. Le Bouc, and S. Babajko Insulin-Like Growth Factor Binding Protein-6 Transgenic Mice: Postnatal Growth, Brain Development, and Reproduction Abnormalities Endocrinology, May 1, 2004; 145(5): 2412 - 2420. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Akgul and C.-P. D. Tu Pentobarbital-mediated Regulation of Alternative Polyadenylation in Drosophila Glutathione S-Transferase D21 mRNAs J. Biol. Chem., February 6, 2004; 279(6): 4027 - 4033. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Qiu, R. Nayak, and D. J. Pintel Alternative Polyadenylation of Adeno-Associated Virus Type 5 RNA within an Internal Intron Is Governed by both a Downstream Element within the Intron 3' Splice Acceptor and an Element Upstream of the P41 Initiation Site J. Virol., January 1, 2004; 78(1): 83 - 93. [Abstract] [Full Text] [PDF]
|
|