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Ricci, E. P., Kucukural, A., Cenik, C., Mercier, B. C., Singh, G., Heyer, E. E., Ashar-Patel, A., Peng, L., & Moore, M. J. (2013). Staufen1 senses overall transcript secondary structure to regulate translation. Nature Structural & Molecular Biology, 21(1), 26–35.

Authors 9
  1. Emiliano P Ricci (first)
  2. Alper Kucukural (additional)
  3. Can Cenik (additional)
  4. Blandine C Mercier (additional)
  5. Guramrit Singh (additional)
  6. Erin E Heyer (additional)
  7. Ami Ashar-Patel (additional)
  8. Lingtao Peng (additional)
  9. Melissa J Moore (additional)
References 52 Referenced 119
  1. Kerner, P., Degnan, S.M., Marchand, L., Degnan, B.M. & Vervoort, M. Evolution of RNA-binding proteins in animals: insights from genome-wide analysis in the sponge Amphimedon queenslandica. Mol. Biol. Evol. 28, 2289–2303 (2011). (10.1093/molbev/msr046) / Mol. Biol. Evol. by P Kerner (2011)
  2. Luo, M., Duchaîne, T.F. & Desgroseillers, L. Molecular mapping of the determinants involved in human Staufen-ribosome association. Biochem. J. 365, 817–824 (2002). (10.1042/bj20020263) / Biochem. J. by M Luo (2002)
  3. Martel, C. et al. Multimerization of Staufen1 in live cells. RNA 16, 585–597 (2010). (10.1261/rna.1664210) / RNA by C Martel (2010)
  4. St Johnston, D., Beuchle, D. & Nüsslein-Volhard, C. Staufen, a gene required to localize maternal RNAs in the Drosophila egg. Cell 66, 51–63 (1991). (10.1016/0092-8674(91)90138-O) / Cell by D St Johnston (1991)
  5. Ferrandon, D., Koch, I., Westhof, E. & Nüsslein-Volhard, C. RNA-RNA interaction is required for the formation of specific bicoid mRNA 3′ UTR–STAUFEN ribonucleoprotein particles. EMBO J. 16, 1751–1758 (1997). (10.1093/emboj/16.7.1751) / EMBO J. by D Ferrandon (1997)
  6. Köhrmann, M. et al. Microtubule-dependent recruitment of Staufen-green fluorescent protein into large RNA-containing granules and subsequent dendritic transport in living hippocampal neurons. Mol. Biol. Cell 10, 2945–2953 (1999). (10.1091/mbc.10.9.2945) / Mol. Biol. Cell by M Köhrmann (1999)
  7. Dugré-Brisson, S. et al. Interaction of Staufen1 with the 5′ end of mRNA facilitates translation of these RNAs. Nucleic Acids Res. 33, 4797–4812 (2005). (10.1093/nar/gki794) / Nucleic Acids Res. by S Dugré-Brisson (2005)
  8. Kim, Y.K., Furic, L., Desgroseillers, L. & Maquat, L.E. Mammalian Staufen1 recruits Upf1 to specific mRNA 3′UTRs so as to elicit mRNA decay. Cell 120, 195–208 (2005). (10.1016/j.cell.2004.11.050) / Cell by YK Kim (2005)
  9. Gong, C. & Maquat, L.E. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470, 284–288 (2011). (10.1038/nature09701) / Nature by C Gong (2011)
  10. Gleghorn, M.L., Gong, C., Kielkopf, C.L. & Maquat, L.E. Staufen1 dimerizes through a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay. Nat. Struct. Mol. Biol. 20, 515–524 (2013). (10.1038/nsmb.2528) / Nat. Struct. Mol. Biol. by ML Gleghorn (2013)
  11. Park, E., Gleghorn, M.L. & Maquat, L. E. Staufen2 functions in Staufen1-mediated mRNA decay by binding to itself and its paralog and promoting UPF1 helicase but not ATPase activity. Proc. Natl. Acad. Sci. USA 110, 405–412 (2013). (10.1073/pnas.1213508110) / Proc. Natl. Acad. Sci. USA by E Park (2013)
  12. Thomas, M.G., Martinez Tosar, L.J., Desbats, M.A., Leishman, C.C. & Boccaccio, G.L. Mammalian Staufen 1 is recruited to stress granules and impairs their assembly. J. Cell Sci. 122, 563–573 (2009). (10.1242/jcs.038208) / J. Cell Sci. by MG Thomas (2009)
  13. Ravel-Chapuis, A. et al. The RNA-binding protein Staufen1 is increased in DM1 skeletal muscle and promotes alternative pre-mRNA splicing. J. Cell Biol. 196, 699–712 (2012). (10.1083/jcb.201108113) / J. Cell Biol. by A Ravel-Chapuis (2012)
  14. Vessey, J.P. et al. A loss of function allele for murine Staufen1 leads to impairment of dendritic Staufen1-RNP delivery and dendritic spine morphogenesis. Proc. Natl. Acad. Sci. USA 105, 16374–16379 (2008). (10.1073/pnas.0804583105) / Proc. Natl. Acad. Sci. USA by JP Vessey (2008)
  15. Furic, L., Maher-Laporte, M. & Desgroseillers, L. A genome-wide approach identifies distinct but overlapping subsets of cellular mRNAs associated with Staufen1- and Staufen2-containing ribonucleoprotein complexes. RNA 14, 324–335 (2008). (10.1261/rna.720308) / RNA by L Furic (2008)
  16. Laver, J.D. et al. Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity. Nucleic Acids Res. 41, 9438–9460 (2013). (10.1093/nar/gkt702) / Nucleic Acids Res. by JD Laver (2013)
  17. Maher-Laporte, M. & Desgroseillers, L. Genome wide identification of Staufen2-bound mRNAs in embryonic rat brains. BMB Rep. 43, 344–348 (2010). (10.5483/BMBRep.2010.43.5.344) / BMB Rep. by M Maher-Laporte (2010)
  18. Kusek, G. et al. Asymmetric segregation of the double-stranded RNA binding protein Staufen2 during mammalian neural stem cell divisions promotes lineage progression. Cell Stem Cell 11, 505–516 (2012). (10.1016/j.stem.2012.06.006) / Cell Stem Cell by G Kusek (2012)
  19. Ferrandon, D., Elphick, L., Nüsslein-Volhard, C. & St Johnston, D. Staufen protein associates with the 3′UTR of bicoid mRNA to form particles that move in a microtubule-dependent manner. Cell 79, 1221–1232 (1994). (10.1016/0092-8674(94)90013-2) / Cell by D Ferrandon (1994)
  20. Kim, Y.K. et al. Staufen1 regulates diverse classes of mammalian transcripts. EMBO J. 26, 2670–2681 (2007). (10.1038/sj.emboj.7601712) / EMBO J. by YK Kim (2007)
  21. Singh, G., Ricci, E.P. & Moore, M.J. RIPiT-Seq: a high-throughput approach for footprinting RNA:protein complexes. Methods 10.1016/j.ymeth.2013.09.013 (2 October 2013).
  22. Ramos, A. et al. RNA recognition by a Staufen double-stranded RNA-binding domain. EMBO J. 19, 997–1009 (2000). (10.1093/emboj/19.5.997) / EMBO J. by A Ramos (2000)
  23. Liu, Z.R., Wilkie, A.M., Clemens, M.J. & Smith, C.W. Detection of double-stranded RNA-protein interactions by methylene blue-mediated photo-crosslinking. RNA 2, 611–621 (1996). / RNA by ZR Liu (1996)
  24. Singh, G. et al. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell 151, 750–764 (2012). (10.1016/j.cell.2012.10.007) / Cell by G Singh (2012)
  25. Miura, P., Shenker, S., Andreu-Agullo, C., Westholm, J.O. & Lai, E.C. Widespread and extensive lengthening of 3′ UTRs in the mammalian brain. Genome Res. 23, 812–825 (2013). (10.1101/gr.146886.112) / Genome Res. by P Miura (2013)
  26. Kucukural, A., Özadam, H., Singh, G., Moore, M.J. & Cenik, C. ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq. Bioinformatics 29, 2485–2486 (2013). (10.1093/bioinformatics/btt428) / Bioinformatics by A Kucukural (2013)
  27. Carmona-Saez, P., Chagoyen, M., Tirado, F., Carazo, J.M. & Pascual-Montano, A. GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biol. 8, R3 (2007). (10.1186/gb-2007-8-1-r3) / Genome Biol. by P Carmona-Saez (2007)
  28. Nogales-Cadenas, R. et al. GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Res. 37, W317–W322 (2009). (10.1093/nar/gkp416) / Nucleic Acids Res. by R Nogales-Cadenas (2009)
  29. Tabas-Madrid, D., Nogales-Cadenas, R. & Pascual-Montano, A. GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. Nucleic Acids Res. 40, W478–W483 (2012). (10.1093/nar/gks402) / Nucleic Acids Res. by D Tabas-Madrid (2012)
  30. Micklem, D.R., Adams, J., Grünert, S. & St Johnston, D. Distinct roles of two conserved Staufen domains in oskar mRNA localization and translation. EMBO J. 19, 1366–1377 (2000). (10.1093/emboj/19.6.1366) / EMBO J. by DR Micklem (2000)
  31. Macchi, P. et al. The brain-specific double-stranded RNA-binding protein Staufen2: nucleolar accumulation and isoform-specific exportin-5-dependent export. J. Biol. Chem. 279, 31440–31444 (2004). (10.1074/jbc.C400226200) / J. Biol. Chem. by P Macchi (2004)
  32. Kiebler, M.A. et al. The mammalian staufen protein localizes to the somatodendritic domain of cultured hippocampal neurons: implications for its involvement in mRNA transport. J. Neurosci. 19, 288–297 (1999). (10.1523/JNEUROSCI.19-01-00288.1999) / J. Neurosci. by MA Kiebler (1999)
  33. Cho, H. et al. Staufen1-mediated mRNA decay functions in adipogenesis. Mol. Cell 46, 495–506 (2012). (10.1016/j.molcel.2012.03.009) / Mol. Cell by H Cho (2012)
  34. Kretz, M. et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493, 231–235 (2013). (10.1038/nature11661) / Nature by M Kretz (2013)
  35. Ghosh, S., Marchand, V., Gáspár, I. & Ephrussi, A. Control of RNP motility and localization by a splicing-dependent structure in oskar mRNA. Nat. Struct. Mol. Biol. 19, 441–449 (2012). (10.1038/nsmb.2257) / Nat. Struct. Mol. Biol. by S Ghosh (2012)
  36. Nott, A., Le Hir, H. & Moore, M.J. Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev. 18, 210–222 (2004). (10.1101/gad.1163204) / Genes Dev. by A Nott (2004)
  37. Wiegand, H.L., Lu, S. & Cullen, B.R. Exon junction complexes mediate the enhancing effect of splicing on mRNA expression. Proc. Natl. Acad. Sci. USA 100, 11327–11332 (2003). (10.1073/pnas.1934877100) / Proc. Natl. Acad. Sci. USA by HL Wiegand (2003)
  38. Ivanov, P.V., Gehring, N.H., Kunz, J.B., Hentze, M.W. & Kulozik, A.E. Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways. EMBO J. 27, 736–747 (2008). (10.1038/emboj.2008.17) / EMBO J. by PV Ivanov (2008)
  39. Marión, R.M., Fortes, P., Beloso, A., Dotti, C. & Ortín, J. A human sequence homologue of Staufen is an RNA-binding protein that is associated with polysomes and localizes to the rough endoplasmic reticulum. Mol. Cell Biol. 19, 2212–2219 (1999). (10.1128/MCB.19.3.2212) / Mol. Cell Biol. by RM Marión (1999)
  40. Wickham, L., Duchaîne, T., Luo, M., Nabi, I.R. & DesGroseillers, L. Mammalian staufen is a double-stranded-RNA- and tubulin-binding protein which localizes to the rough endoplasmic reticulum. Mol. Cell Biol. 19, 2220–2230 (1999). (10.1128/MCB.19.3.2220) / Mol. Cell Biol. by L Wickham (1999)
  41. Monshausen, M. et al. Two rat brain staufen isoforms differentially bind RNA. J. Neurochem. 76, 155–165 (2001). (10.1046/j.1471-4159.2001.00061.x) / J. Neurochem. by M Monshausen (2001)
  42. Elbarbary, R.A., Li, W., Tian, B. & Maquat, L.E. STAU1 binding 3′ UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown. Genes Dev. 27, 1495–1510 (2013). (10.1101/gad.220962.113) / Genes Dev. by RA Elbarbary (2013)
  43. Hartman, T.R. et al. RNA helicase A is necessary for translation of selected messenger RNAs. Nat. Struct. Mol. Biol. 13, 509–516 (2006). (10.1038/nsmb1092) / Nat. Struct. Mol. Biol. by TR Hartman (2006)
  44. Villacé, P., Marión, R.M. & Ortín, J. The composition of Staufen-containing RNA granules from human cells indicates their role in the regulated transport and translation of messenger RNAs. Nucleic Acids Res. 32, 2411–2420 (2004). (10.1093/nar/gkh552) / Nucleic Acids Res. by P Villacé (2004)
  45. Darnell, J.C. et al. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell 146, 247–261 (2011). (10.1016/j.cell.2011.06.013) / Cell by JC Darnell (2011)
  46. Comery, T.A. et al. Abnormal dendritic spines in fragile X knockout mice: maturation and pruning deficits. Proc. Natl. Acad. Sci. USA 94, 5401–5404 (1997). (10.1073/pnas.94.10.5401) / Proc. Natl. Acad. Sci. USA by TA Comery (1997)
  47. Gruber, A.R., Lorenz, R., Bernhart, S.H., Neuböck, R. & Hofacker, I.L. The Vienna RNA websuite. Nucleic Acids Res. 36, W70–W74 (2008). (10.1093/nar/gkn188) / Nucleic Acids Res. by AR Gruber (2008)
  48. Ricci, E.P. et al. Translation of intronless RNAs is strongly stimulated by the Epstein-Barr virus mRNA export factor EB2. Nucleic Acids Res. 37, 4932–4943 (2009). (10.1093/nar/gkp497) / Nucleic Acids Res. by EP Ricci (2009)
  49. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009). (10.1093/bioinformatics/btp120) / Bioinformatics by C Trapnell (2009)
  50. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009). (10.1186/gb-2009-10-3-r25) / Genome Biol. by B Langmead (2009)
  51. Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010). (10.1093/bioinformatics/btq033) / Bioinformatics by AR Quinlan (2010)
  52. McCarthy, D.J., Chen, Y. & Smyth, G.K. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 40, 4288–4297 (2012). (10.1093/nar/gks042) / Nucleic Acids Res. by DJ McCarthy (2012)
Dates
Type When
Created 11 years, 8 months ago (Dec. 15, 2013, 2:14 p.m.)
Deposited 2 years, 3 months ago (May 19, 2023, 12:35 a.m.)
Indexed 2 weeks, 5 days ago (Aug. 12, 2025, 6:08 p.m.)
Issued 11 years, 8 months ago (Dec. 15, 2013)
Published 11 years, 8 months ago (Dec. 15, 2013)
Published Online 11 years, 8 months ago (Dec. 15, 2013)
Published Print 11 years, 7 months ago (Jan. 1, 2014)
Funders 0

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@article{Ricci_2013, title={Staufen1 senses overall transcript secondary structure to regulate translation}, volume={21}, ISSN={1545-9985}, url={http://dx.doi.org/10.1038/nsmb.2739}, DOI={10.1038/nsmb.2739}, number={1}, journal={Nature Structural & Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Ricci, Emiliano P and Kucukural, Alper and Cenik, Can and Mercier, Blandine C and Singh, Guramrit and Heyer, Erin E and Ashar-Patel, Ami and Peng, Lingtao and Moore, Melissa J}, year={2013}, month=dec, pages={26–35} }