XThe frustrated gene: Origins of eukaryotic gene expression

Cell

Volumn 155, Issue 4, 2013, Pages 744-

  Madhani, Hiten D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; NUCLEIC ACID;

CHROMATIN; DNA DETERMINATION; EUKARYOTE; GENE EXPRESSION; PRIORITY JOURNAL; PROKARYOTE; REVIEW; SPLICEOSOME; TRANSPOSON;

EUKARYOTA; PROKARYOTA;

EID: 84887948238     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.10.003     Document Type: Note

References (42)

1. R. Ammar, D. Torti, K. Tsui, M. Gebbia, T. Durbic, G.D. Bader, G. Giaever, and C. Nislow Chromatin is an ancient innovation conserved between Archaea and Eukarya Elife 1 2012 e00078
2. Y. Araki, S. Takahashi, T. Kobayashi, H. Kajiho, S. Hoshino, and T. Katada Ski7p G protein interacts with the exosome and the Ski complex for 3′-to-5′ mRNA decay in yeast EMBO J. 20 2001 4684 4693
3. A.T. Belew, V.M. Advani, and J.D. Dinman Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast Nucleic Acids Res. 39 2011 2799 2808
4. H.M. Bourbon Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex Nucleic Acids Res. 36 2008 3993 4008
5. H. Cerutti, and J.A. Casas-Mollano On the origin and functions of RNA-mediated silencing: from protists to man Curr. Genet. 50 2006 81 99
6. N. Craig, R. Craigie, M. Gellert, and A. Lambowitz Mobile Genetic Elements II 2002 ASM Press Washington, DC
7. B.R. Cullen Nuclear mRNA export: insights from virology Trends Biochem. Sci. 28 2003 419 424
8. S. Daffis, K.J. Szretter, J. Schriewer, J. Li, S. Youn, J. Errett, T.Y. Lin, S. Schneller, R. Zust, and H. Dong 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members Nature 468 2010 452 456
9. R. Dawkins The Selfish Gene 1976 Oxford University Press Oxford, UK
10. S.W. Ding, and O. Voinnet Antiviral immunity directed by small RNAs Cell 130 2007 413 426
11. P.A. Dumesic, P. Natarajan, C. Chen, I.A. Drinnenberg, B.J. Schiller, J. Thompson, J.J. Moresco, J.R. Yates 3rd, D.P. Bartel, and H.D. Madhani Stalled spliceosomes are a signal for RNAi-mediated genome defense Cell 152 2013 957 968
12. E. Ehrenfeld Poliovirus-induced inhibition of host-cell protein synthesis Cell 28 1982 435 436
13. W.P. Galej, C. Oubridge, A.J. Newman, and K. Nagai Crystal structure of Prp8 reveals active site cavity of the spliceosome Nature 493 2013 638 643
14. S.G. Gornik, K.L. Ford, T.D. Mulhern, A. Bacic, G.I. McFadden, and R.F. Waller Loss of nucleosomal DNA condensation coincides with appearance of a novel nuclear protein in dinoflagellates Curr. Biol. 22 2012 2303 2312
15. U.F. Greber, M. Willetts, P. Webster, and A. Helenius Stepwise dismantling of adenovirus 2 during entry into cells Cell 75 1993 477 486
16. D.A. Hickey Selfish DNA: a sexually-transmitted nuclear parasite Genetics 101 1982 519 531
17. J. Hollien Evolution of the unfolded protein response Biochim. Biophys. Acta 1833 2013 2458 2463
18. E.R. James, and D.R. Green Infection and the origins of apoptosis Cell Death Differ. 9 2002 355 357
19. L. Joshua-Tor, and G.J. Hannon Ancestral roles of small RNAs: an Ago-centric perspective Cold Spring Harb. Perspect. Biol. 3 2011 a003772
20. E.V. Koonin The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol. Direct 1 2006 22
21. J.A. Law, J. Du, C.J. Hale, S. Feng, K. Krajewski, A.M. Palanca, B.D. Strahl, D.J. Patel, and S.E. Jacobsen Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1 Nature 498 2013 385 389
22. H. Le Hir, and B. Séraphin EJCs at the heart of translational control Cell 133 2008 213 216
23. V.C. Li, J.C. Davis, K. Lenkov, B. Bolival, M.T. Fuller, and D.A. Petrov Molecular evolution of the testis TAFs of Drosophila Mol. Biol. Evol. 26 2009 1103 1116
24. Y.M. Loo, and M. Gale Jr. Immune signaling by RIG-I-like receptors Immunity 34 2011 680 692
25. M. Lynch, and J.S. Conery The origins of genome complexity Science 302 2003 1401 1404
26. H.D. Madhani, and C. Guthrie A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome Cell 71 1992 803 817
27. K.S. Makarova, Y.I. Wolf, and E.V. Koonin Comparative genomics of defense systems in archaea and bacteria Nucleic Acids Res. 41 2013 4360 4377
28. K. Nakano, T. Ando, M. Yamagishi, K. Yokoyama, T. Ishida, T. Ohsugi, Y. Tanaka, D.W. Brighty, and T. Watanabe Viral interference with host mRNA surveillance, the nonsense-mediated mRNA decay (NMD) pathway, through a new function of HTLV-1 Rex: implications for retroviral replication Microbes Infect. 15 2013 491 505
29. R. Parker RNA degradation in Saccharomyces cerevisae Genetics 191 2012 671 702
30. J.C. Peng, and H. Lin Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism Curr. Opin. Cell Biol. 25 2013 190 194
31. C.S. Pikaard, J.R. Haag, O.M. Pontes, T. Blevins, and R. Cocklin A transcription fork model for Pol IV and Pol V-dependent RNA-directed DNA methylation Cold Spring Harb. Symp. Quant. Biol. 77 2013 205 212
32. I.B. Rogozin, L. Carmel, M. Csuros, and E.V. Koonin Origin and evolution of spliceosomal introns Biol. Direct 7 2012 11
33. S.L. Roth, N. Malani, and F.D. Bushman Gammaretroviral integration into nucleosomal target DNA in vivo J. Virol. 85 2011 7393 7401
34. S.A. Shabalina, and E.V. Koonin Origins and evolution of eukaryotic RNA interference Trends Ecol. Evol. 23 2008 578 587
35. S. Shuman What messenger RNA capping tells us about eukaryotic evolution Nat. Rev. Mol. Cell Biol. 3 2002 619 625
36. M. Smolle, J.L. Workman, and S. Venkatesh reSETting chromatin during transcription elongation Epigenetics 8 2013 10 15
37. R. van der Veen, A.C. Arnberg, G. van der Horst, L. Bonen, H.F. Tabak, and L.A. Grivell Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro Cell 44 1986 225 234
38. D. Walsh, M.B. Mathews, and I. Mohr Tinkering with translation: protein synthesis in virus-infected cells Cold Spring Harb. Perspect. Biol. 5 2013 a012351
39. M. Werner, E. Purta, K.H. Kaminska, I.A. Cymerman, D.A. Campbell, B. Mittra, J.R. Zamudio, N.R. Sturm, J. Jaworski, and J.M. Bujnicki 2′-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family Nucleic Acids Res. 39 2011 4756 4768
40. Y.T. Yu, P.A. Maroney, E. Darzynkiwicz, and T.W. Nilsen U6 snRNA function in nuclear pre-mRNA splicing: a phosphorothioate interference analysis of the U6 phosphate backbone RNA 1 1995 46 54
41. F. Zhang, J. Wang, J. Xu, Z. Zhang, B.S. Koppetsch, N. Schultz, T. Vreven, C. Meignin, I. Davis, and P.D. Zamore UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery Cell 151 2012 871 884
42. D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, and S. Henikoff Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription Nat. Genet. 39 2007 61 69