An epitranscriptomic switch at the 5′-UTR controls genome selection during HIV-1 genomic RNA packaging
Camila Pereira-Montecinos, Daniela Toro-Ascuy, Cecilia Rojas-Fuentes, SebastiánRiquelme-Barrios, Bárbara Rojas-Araya, Francisco García-de-Gracia, PaulinaAguilera-Cortés, Catarina Ananías-Sáez, Grégoire de Bisschop, Jonás Chaniderman, Mónica L. Acevedo, Bruno Sargueil, Fernando Valiente-Echeverría, Ricardo Soto-Rifo
bioRxiv 676031; doi: https://doi.org/10.1101/676031

DISC1 promotes translation maintenance during sodium arsenite-induced oxidative stress.
Fuentes-Villalobos F, Farkas C, Riquelme-Barrios S, Armijo ME, Soto-Rifo R, Pincheira R, Castro AF.
Biochim Biophys Acta Gene Regul Mech. 2019 Jun;1862(6):657-669. doi: 10.1016/j.bbagrm.2019.05.001. Epub 2019 May 7.

Salmon cells SHK-1 internalize infectious pancreatic necrosis virus by macropinocytosis.
Levicán-Asenjo J, Soto-Rifo R, Aguayo F, Gaggero A, Leon O.
J Fish Dis. 2019 Jul;42(7):1035-1046. doi: 10.1111/jfd.13009. Epub 2019 May 2.


A Rev-CBP80-eIF4AI complex drives Gag synthesis from the HIV-1 unspliced mRNA.
Toro-Ascuy D, Rojas-Araya B, García-de-Gracia F, Rojas-Fuentes C, Pereira-Montecinos C, Gaete-Argel A, Valiente-Echeverría F, Ohlmann T, Soto-Rifo R.
Nucleic Acids Res. 2018 Nov 30;46(21):11539-11552. doi: 10.1093/nar/gky851.

Emerging Roles of N6-Methyladenosine on HIV-1 RNA Metabolism and Viral Replication.
Riquelme-Barrios S, Pereira-Montecinos C, Valiente-Echeverría F, Soto-Rifo R.
Front Microbiol. 2018 Mar 28;9:576. doi: 10.3389/fmicb.2018.00576. eCollection 2018. Review.

Differences in the internalization of self-inactivating VSVG-pseudotyped murine leukemia virus-based vectors in human and murine cells.
Acevedo ML, García-de Gracia F, Miranda-Cárdenas C, Soto-Rifo R, Aguayo F, León O.
J Virol Methods. 2018 May;255:14-22. doi: 10.1016/j.jviromet.2018.02.005. Epub 2018 Feb 6.


Infectious pancreatic necrosis virus enters CHSE-214 cells via macropinocytosis.
Levican J, Miranda-Cárdenas C, Soto-Rifo R, Aguayo F, Gaggero A, León O.
Sci Rep. 2017 Jun 8;7(1):3068. doi: 10.1038/s41598-017-03036-w.

Epitranscriptomic regulation of viral replication.
Pereira-Montecinos C, Valiente-Echeverría F, Soto-Rifo R.
Biochim Biophys Acta. 2017 Feb 17;1860(4):460-471. doi: 10.1016/j.bbagrm.2017.02.002. Review.

microRNAs stimulate translation initiation mediated by HCV-like IRESes.
Mengardi C, Limousin T, Ricci EP, Soto-Rifo R, Decimo D, Ohlmann T.
Nucleic Acids Res. 2017 Jan 10. pii: gkw1345. doi: 10.1093/nar/gkw1345


Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries.
Toro-Ascuy D, Rojas-Araya B, Valiente-Echeverría F, Soto-Rifo R.
Viruses. 2016 Nov 23;8(11). pii: E320. Review.

Who Regulates Whom? An Overview of RNA Granules and Viral Infections
Natalia Poblete-Durán, Yara Prades-Pérez, Jorge Vera-Otarola, Ricardo Soto-Rifo and Fernando Valiente-Echeverría
Viruses 2016, 8(7), 180; doi:10.3390/v8070180

DEAD-box RNA helicase DDX3 connects CRM1-dependent nuclear export and translation of the HIV-1 unspliced mRNA through its N-terminal domain.
Fröhlich A, Rojas-Araya B, Pereira-Montecinos C, Dellarossa A, Toro-Ascuy D, Prades-Pérez Y, García-de-Gracia F, Garcés-Alday A, Rubilar PS, Valiente-Echeverría F, Ohlmann T, Soto-Rifo R.
Biochim Biophys Acta. 2016 Mar 21. pii: S1874-9399(16)30054-2. doi: 10.1016/j.bbagrm.2016.03.009


HIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA
Lara Ajamian, Karen Abel, Shringar Rao, Kishanda Vyboh, Francisco García-de-Gracia, Ricardo Soto-Rifo, Andreas E. Kulozik, Niels H. Gehring and Andrew J. Mouland
Biomolecules. 2015 5, 2808-2839. doi: 10.3390/biom5042808.

Translational Control of the HIV Unspliced Genomic RNA.
Rojas-Araya B, Ohlmann T* and
Soto-Rifo R*
Viruses. 2015 Aug 4;7(8):4326-51. doi: 10.3390/v7082822.

* Corresponding authors

RNA helicase DDX3: at the crossroad of viral replication and antiviral immunity.
Fernando Valiente-Echeverría*, Marcela A. Hermoso and Ricardo Soto-Rifo*
Reviews in Medical Virology 4 Jul 2015 DOI: 10.1002/rmv.1845
* Corresponding authors

Tobacco Smoke Activates Human Papillomavirus 16 p97 Promoter and Cooperates with High-Risk E6/E7 for Oxidative DNA Damage in Lung Cells.
Peña N, Carrillo D, Muñoz JP, Chnaiderman J, Urzúa U, León O, Tornesello ML, Corvalán AH, Ricardo Soto-Rifo, Aguayo F.
PLoS One. 2015 Apr 1;10(4):e0123029. doi: 10.1371/journal.pone.0123029. eCollection 2015.


HIV-2 genomic RNA accumulates in stress granules in the absence of active translation
Ricardo Soto-Rifo*, Fernando Valiente-Echeverria, Paulina S. Rubilar, Francisco Garcia-de-Gracia, Emiliano P. Ricci, Taran Limousin, Didier Décimo, Andrew J. Mouland and Théophile Ohlmann*
Nucleic Acids Res. 2014 Nov 10;42(20):12861-75
* Corresponding authors


The DEAD-box helicase DDX3 substitutes for the cap-binding protein eIF4E to promote compartmentalized translation initiation of the HIV-1 genomic RNA.
Soto-Rifo R*, Rubilar PS, Ohlmann T*.
Nucleic Acids Res. 2013 Jul;41(12):6286-99. doi: 10.1093/nar/gkt306. Epub 2013 Apr 28.
*Corresponding authors

The role of the DEAD-box RNA helicase DDX3 in mRNA metabolism.
Soto-Rifo R*, Ohlmann T.
Wiley Interdiscip Rev RNA. 2013 Jul-Aug;4(4):369-85. doi: 10.1002/wrna.1165. Epub 2013 Apr 18.
*Corresponding author

miRNA repression of translation in vitro takes place during 43S ribosomal scanning.
Ricci EP*, Limousin T*, Soto-Rifo R*, Rubilar PS, Decimo D, Ohlmann T.
Nucleic Acids Res. 2013 Jan 7;41(1):586-98. doi: 10.1093/nar/gks1076. Epub 2012 Nov 17.
*Co-first authors, equal contributions

Translation initiation is driven by different mechanisms on the HIV-1 and HIV-2 genomic RNAs.
de Breyne S, Soto-Rifo R, López-Lastra M, Ohlmann T.
Virus Res. 2013 Feb;171(2):366-81. doi: 10.1016/j.virusres.2012.10.006. Epub 2012 Oct 16. Review.


DEAD-box protein DDX3 associates with eIF4F to promote translation of selected mRNAs.
Soto-Rifo R, Rubilar PS, Limousin T, de Breyne S, Décimo D, Ohlmann T.
EMBO J. 2012 Sep 12;31(18):3745-56. doi: 10.1038/emboj.2012.220. Epub 2012 Aug 7.

The Andes hantavirus NSs protein is expressed from the viral small mRNA by a leaky scanning mechanism.
Vera-Otarola J, Solis L, Soto-Rifo R, Ricci EP, Pino K, Tischler ND, Ohlmann T, Darlix JL, López-Lastra M.
J Virol. 2012 Feb;86(4):2176-87. doi: 10.1128/JVI.06223-11. Epub 2011 Dec 7.

Different effects of the TAR structure on HIV-1 and HIV-2 genomic RNA translation.
Soto-Rifo R, Limousin T, Rubilar PS, Ricci EP, Décimo D, Moncorgé O, Trabaud MA, André P, Cimarelli A, Ohlmann T.
Nucleic Acids Res. 2012 Mar;40(6):2653-67. doi: 10.1093/nar/gkr1093. Epub 2011 Nov 24.

Functional mechanisms of the cellular prion protein (PrP(C)) associated anti-HIV-1 properties.
Alais S, Soto-Rifo R, Balter V, Gruffat H, Manet E, Schaeffer L, Darlix JL, Cimarelli A, Raposo G, Ohlmann T, Leblanc P.
Cell Mol Life Sci. 2012 Apr;69(8):1331-52. doi: 10.1007/s00018-011-0879-z. Epub 2011 Nov 11.


Activation of a microRNA response in trans reveals a new role for poly(A) in translational repression.
Ricci EP, Limousin T, Soto-Rifo R, Allison R, Pöyry T, Decimo D, Jackson RJ, Ohlmann T.
Nucleic Acids Res. 2011 Jul;39(12):5215-31. doi: 10.1093/nar/gkr086. Epub 2011 Mar 8.


The 3' untranslated region of the Andes hantavirus small mRNA functionally replaces the poly(A) tail and stimulates cap-dependent translation initiation from the viral mRNA.
Vera-Otarola J, Soto-Rifo R, Ricci EP, Ohlmann T, Darlix JL, López-Lastra M.
J Virol. 2010 Oct;84(19):10420-4. doi: 10.1128/JVI.01270-10. Epub 2010 Jul 21.


Mechanism of HIV-1 Tat RNA translation and its activation by the Tat protein.
Charnay N, Ivanyi-Nagy R, Soto-Rifo R, Ohlmann T, López-Lastra M, Darlix JL.
Retrovirology. 2009 Aug 11;6:74. doi: 10.1186/1742-4690-6-74.

Structural and functional diversity of viral IRESes.
Balvay L, Soto Rifo R, Ricci EP, Decimo D, Ohlmann T.
Biochim Biophys Acta. 2009 Sep-Oct;1789(9-10):542-57. doi: 10.1016/j.bbagrm.2009.07.005. Epub 2009 Jul 24. Review.


Lentiviral RNAs can use different mechanisms for translation initiation.
Ricci EP, Soto Rifo R, Herbreteau CH, Decimo D, Ohlmann T.
Biochem Soc Trans. 2008 Aug;36(Pt 4):690-3. doi: 10.1042/BST0360690.


Back to basics: the untreated rabbit reticulocyte lysate as a competitive system to recapitulate cap/poly(A) synergy and the selective advantage of IRES-driven translation.
Soto Rifo R, Ricci EP, Décimo D, Moncorgé O, Ohlmann T.
Nucleic Acids Res. 2007;35(18):e121. Epub 2007 Sep 18.

Homozygous mutation of AURKC yields large-headed polyploid spermatozoa and causes male infertility.
Dieterich K, Soto Rifo R, Faure AK, Hennebicq S, Ben Amar B, Zahi M, Perrin J, Martinez D, Sèle B, Jouk PS, Ohlmann T, Rousseaux S, Lunardi J, Ray PF.
Nat Genet. 2007 May;39(5):661-5. Epub 2007 Apr 15.