267
Views
12
CrossRef citations to date
0
Altmetric
Articles

Structural model of the complete poly(A) region of HIV-1 pre-mRNA

, , &
Pages 1044-1056 | Received 24 Apr 2012, Accepted 31 Jul 2012, Published online: 11 Sep 2012

References

  • Abbink , T.E. and Berkhout , B. 2003 . A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon . Journal of Biological Chemistry , 278 : 11601 – 11611 .
  • Arhin , G.K. , Boots , M. , Bagga , P.S. , Milcarek , C. and Wilusz , J. 2002 . Downstream sequence elements with different affinities for the hnRNP H/H’ protein influence the processing efficiency of mammalian polyadenylation signals . Nucleic Acids Research , 30 : 1842 – 1850 .
  • Ashe , M.P. , Griffin , P. , James , W. and Proudfoot , N.J. 1995 . Poly(A) site selection in the HIV-1 provirus: Inhibition of promoter-proximal polyadenylation by the downstream major splice donor site . Genes and Development , 9 : 3008 – 3025 .
  • Ashe , M.P. , Pearson , L.H. and Proudfoot , N.J. 1997 . The HIV-1 5’ LTR poly(A) site is inactivated by U1 snRNP interaction with the downstream major splice donor site . EMBO Journal , 16 : 5752 – 5763 .
  • Bagga , P.S. , Arhin , G.K. and Wilusz , J. 1998 . DSEF-1 is a member of the hnRNP H family of RNA-binding proteins and stimulates pre-mRNA cleavage and polyadenylation in vitro . Nucleic Acids Research , 26 : 5343 – 5350 .
  • Bagga , P.S. , Ford , L.P. , Chen , F. and Wilusz , J. 1995 . The G-rich auxiliary downstream element has distinct sequence and position requirements and mediates efficient 3’ end pre-mRNA processing through a trans-acting factor . Nucleic Acids Research , 23 : 1625 – 1631 .
  • Berkhout , B. , Klaver , B. and Das , A.T. 1995 . A conserved hairpin structure predicted for the poly(A) signal of human and simian immunodeficiency viruses . Virology , 207 : 276 – 281 .
  • Brown , P.H. , Tiley , L.S. and Cullen , B.R. 1991 . Efficient polyadenylation within the human immunodeficiency virus type 1 long terminal repeat requires flanking U3-specific sequences . Journal of Virology , 65 : 3340 – 3343 .
  • Bryan , T.M. and Baumann , P. 2011 . G-quadruplexes: From guanine gels to chemotherapeutics . Molecular Biotechnology , 49 : 198 – 208 .
  • Cherrington , J. and Ganem , D. 1992 . Regulation of polyadenylation in human immunodeficiency virus (HIV): Contributions of promoter proximity and upstream sequences . EMBO Journal , 11 : 1513 – 1524 .
  • Colgan , D.F. and Manley , J.L. 1997 . Mechanism and regulation of mRNA polyadenylation . Genes & Development , 11 : 2755 – 2766 .
  • Damgaard , C.K. , Andersen , E.S. , Knudsen , B. , Gorodkin , J. and Kjems , J. 2004 . RNA interactions in the 5’ region of the HIV-1 genome . Journal of Molecular Biology , 336 : 369 – 379 .
  • Dantonel , J.-C. , Murthy , K.G. , Manley , J.L. and Tora , L. 1997 . Transcription factor TFIID recruits factor CPSF for formation of 3’ end of mRNA . Nature , 389 : 399 – 402 .
  • Das , A.T. , Klaver , B. and Berkhout , B. 1999 . A hairpin structure in the R region of the human immunodeficiency virus type 1 RNA genome is instrumental in polyadenylation site selection . Journal of Virology , 73 : 81 – 91 .
  • Das , A.T. , Klaver , B. , Klasens , B.I. , van Wamel , J.L. and Berkhout , B. 1997 . A conserved hairpin motif in the R-U5 region of the human immunodeficiency virus type 1 RNA genome is essential for replication . Journal of Virology , 71 : 2346 – 2356 .
  • Decorsière , A. , Cayrel , A. , Vagner , S. and Millevoi , S. 2011 . Essential role for the interaction between hnRNP H/F and a G quadruplex in maintaining p53 pre-mRNA 3’-end processing and function during DNA damage . Genes & Development , 25 : 220 – 225 .
  • DeZazzo , J.D. , Kilpatrick , J.E. and Imperiale , M.J. 1991 . Involvement of long terminal repeat U3 sequences overlapping the transcription control region in human immunodeficiency virus type 1 mRNA 3’ end formation . Molecular and Cellular Biology , 11 : 1624 – 1630 .
  • Gee , A.H. , Kasprzak , W. and Shapiro , B.A. 2006 . Structural differentiation of the HIV-1 polyA signals . Journal of Biomolecular Structure and Dynamics , 23 : 417 – 428 .
  • Gilmartin , G.M. , Fleming , E.S. and Oetjen , J. 1992 . Activation of HIV-1 pre-mRNA 3’ processing in vitro requires both an upstream element and TAR . EMBO Journal , 11 : 4419 – 4428 .
  • Gilmartin , G.M. , Fleming , E.S. , Oetjen , J. and Graveley , B.R. 1995 . CPSF recognition of an HIV-1 mRNA 3’-processing enhancer: Multiple sequence contacts involved in poly(A) site definition . Genes & Development , 9 : 72 – 83 .
  • Guédin , A. , Gros , J. , Alberti , P. and Mergny , J.-L. 2010 . How long is too long? Effects of loop size on G-quadruplex stability . Nucleic Acids Research , 38 : 7858 – 7868 .
  • Isel , C. , Ehresmann , C. and Marquet , R. 2010 . Initiation of HIV reverse transcription . Viruses , 2 : 213 – 243 .
  • Kasprzak , W. , Bindewald , E. and Shapiro , B.A. 2005 . Structural polymorphism of the HIV-1 leader region explored by computational methods . Nucleic Acids Research , 33 : 7151 – 7163 .
  • Kaufmann , I. , Martin , G. , Friedlein , A. , Langen , H. and Keller , W. 2004 . Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase . EMBO Journal , 23 : 616 – 626 .
  • Klasens , B.I. , Das , A.T. and Berkhout , B. 1998 . Inhibition of polyadenylation by stable RNA secondary structure . Nucleic Acids Research , 26 : 1870 – 1876 .
  • Klasens , B.I. , Thiesen , M. , Virtanen , A. and Berkhout , B. 1999 . The ability of the HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structure . Nucleic Acids Research , 27 : 446 – 454 .
  • Kliewer , S. , Garcia , J. , Pearson , L. , Soultanakis , E. , Dasgupta , A. and Gaynor , R. 1989 . Multiple transcriptional regulatory domains in the human immunodeficiency virus type 1 long terminal repeat are involved in basal and E1A/E1B-induced promoter activity . Journal of Virology , 63 : 4616 – 4625 .
  • Kumari , S. , Bugaut , A. and Balasubramanian , S. 2008 . Position and stability are determining factors for translation repression by an RNA G-quadruplex-forming sequence within the 5’ UTR of the NRAS proto-oncogene . Biochemistry , 47 : 12664 – 12669 .
  • Mandel , C.R. , Bai , Y. and Tong , L. 2008 . Protein factors in pre-mRNA 3’-end processing . Cellular and Molecular Life Sciences , 65 : 1099 – 1122 .
  • Markham , N.R. and Zuker , M. 2008 . UNAFold: Software for nucleic acid folding and hybridization . Methods in Molecular Biology , 453 : 3 – 31 .
  • Martadinata , H. , Heddi , B. , Lim , K.W. and Phan , A.T. 2011 . Structure of long human telomeric RNA (TERRA): G-quadruplexes formed by four and eight UUAGGG repeats are stable building blocks . Biochemistry , 50 : 6455 – 6461 .
  • McCracken , S. , Fong , N. , Yankulov , K. , Ballantyne , S. , Pan , G. , Greenblatt , J. , … and Bentley , D.L. 1997 . The C-terminal domain of RNA polymerase II couples mRNA processing to transcription . Nature , 385 : 357 – 361 .
  • Millevoi , S. , Decorsière , A. , Loulergue , C. , Iacovoni , J. , Bernat , S. , Antoniou , M. and Vagner , S. 2009 . A physical and functional link between splicing factors promotes pre-mRNA 3’ end processing . Nucleic Acids Research , 37 : 4672 – 4683 .
  • Millevoi , S. and Vagner , S. 2010 . Molecular mechanisms of eukaryotic pre-mRNA 3’ end processing regulation . Nucleic Acids Research , 38 : 2757 – 2774 .
  • Morris , M.J. , Negishi , Y. , Pazsint , C. , Schonhoft , J.D. and Basu , S. 2010 . An RNA G-quadruplex is essential for cap-independent translation initiation in human VEGF IRES . Journal of the American Chemical Society , 132 : 17831 – 17839 .
  • Neidle , S. 2009 . The structures of quadruplex nucleic acids and their drug complexes . Current Opinion in Structural Biology , 19 : 239 – 250 .
  • Ooms , M. , Abbink , T.E. , Pham , C. and Berkhout , B. 2007 . Circularization of the HIV-1 RNA genome . Nucleic Acids Research , 35 : 5253 – 5261 .
  • Paillart , J.C. , Dettenhofer , M. , Yu , X.-f. , Ehresmann , C. , Ehresmann , B. and Marquet , R. 2004 . First snapshots of the HIV-1 RNA structure in infected cells and in virions . Journal of Biological Chemistry , 279 : 48397 – 48403 .
  • Pereira , L.A. , Bentley , K. , Peeters , A. , Churchill , M.J. and Deacon , N.J. 2000 . A compilation of cellular transcription factor interactions with the HIV-1 LTR promoter . Nucleic Acids Research , 28 : 663 – 668 .
  • Potyahaylo , A. , Kolomiets , I. , Zarudnaya , M. and Hovorun , D. 2009 . Database of the secondary structures of HIV-1 genome control elements . FEBS Journal , 276 ( Suppl. 1 ) : 119
  • Proudfoot , N.J. 2011 . Ending the message: Poly(A) signals then and now . Genes & Development , 25 : 1770 – 1782 .
  • Ramírez de Arellano , E. , Soriano , V. , Alcamil , J. and Holguín , A. 2006 . New findings on transcription regulation across different HIV-1 subtypes . AIDS Reviews , 8 : 9 – 16 .
  • Saadatmand , J. , Niu , M. , Kleiman , L. and Guo , F. 2009 . The contribution of the primer activation signal to differences between Gag- and NCp7-facilitated tRNALys3 annealing in HIV-1 . Virology , 391 : 334 – 341 .
  • Sakuragi , J. , Sakuragi , S. and Shioda , T. 2007 . Minimal region sufficient for genome dimerization in the human immunodeficiency virus type 1 virion and its potential roles in the early stages of viral replication . Journal of Virology , 81 : 7985 – 7992 .
  • Valsamakis , A. , Schek , N. and Alwine , J.C. 1992 . Elements upstream of the AAUAAA within the human immunodeficiency virus polyadenylation signal are required for efficient polyadenylation in vitro . Molecular and Cellular Biology , 12 : 3699 – 3705 .
  • Valsamakis , A. , Zeichner , S. , Carswell , S. and Alwine , J.C. 1991 . The human immunodeficiency virus type 1 polyadenylylation signal: a 3’ long terminal repeat element upstream of the AAUAAA necessary for efficient polyadenylylation . Proceedings of the National Academy of Sciences USA , 88 : 2108 – 2112 .
  • Vrolijk , M.M. , Harwig , A. , Berkhout , B. and Das , A.T. 2009 . Destabilization of the TAR hairpin leads to extension of the polyA hairpin and inhibition of HIV-1 polyadenylation . Retrovirology , 6 : 13
  • Wahle , E. and Rüegsegger , U. 1999 . 3’-End processing of pre-mRNA in eukaryotes . FEMS Microbiology Reviews , 23 : 277 – 295 .
  • Watts , J.M. , Dang , K.K. , Gorelick , R.J. , Leonard , C.W. , Bess , J.W. Jr , Swanstrom , R. , … and Weeks , K.M. 2009 . Architecture and secondary structure of an entire HIV-1 RNA genome . Nature , 460 : 711 – 716 .
  • Weichs an der Glon , C. , Monks , J. and Proudfoot , N.J. 1991 . Occlusion of the HIV poly(A) site . Genes & Development , 5 : 244 – 253 .
  • Wilkinson , K.A. , Gorelick , R.J. , Vasa , S.M. , Guex , N. , Rein , A. , Mathews , D.H. , … and Weeks , K.M. 2008 . High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states . PLoS Biology , 6 : e96
  • Zarudnaya , M.I. , Kolomiets , I.M. , Potyahaylo , A.L. and Hovorun , D.M. 2003 . Downstream elements of mammalian pre-mRNA polyadenylation signals: Primary, secondary and higher-order structures . Nucleic Acids Research , 31 : 1375 – 1386 .
  • Zarudnaya , M.I. , Potyahaylo , A.L. , Kolomiets , I.M. and Hovorun , D.М. 2002 . Auxiliary elements of mammalian pre-mRNAs polyadenylation signals . Biopolymers and Cell , 18 : 500 – 517 .
  • Zarudnaya , M.I. , Potyahaylo , A.L. , Otenko , V.V. , Kolomiyets , I.N. and Hovorun , D.М. 2011 . The secondary structure of сore poly(A) signal of human immunodeficiency virus pre-mRNA . Reports of the National Academy of Sciences of Ukraine , 4 : 170 – 176 . (in Russian)
  • Zhang , A.Y. , Bugaut , A. and Balasubramanian , S. 2011 . A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology . Biochemistry , 50 : 7251 – 7258 .
  • Zhao , J. , Hyman , L. and Moore , C. 1999 . Formation of mRNA 3’ ends in eukaryotes: Mechanism, regulation, and interrelationships with other steps in mRNA synthesis . Microbiology and Molecular Biology Reviews , 63 : 405 – 445 .
  • Zuker , M. 2003 . Mfold web server for nucleic acid folding and hybridization prediction . Nucleic Acids Research , 31 : 3406 – 3415 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.