Nuclear export as a key arbiter of "mRNA identity" in eukaryotes

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1819, Issue 6, 2012, Pages 566-577

  Palazzo, Alexander F ^a   Akef, Abdalla ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

ALREX; Coupling; MRNA export; MRNA identity; SSCR; TREX

Indexed keywords

MESSENGER RNA; SIGNAL PEPTIDE; TRANSCRIPTION ELONGATION FACTOR;

CELL NUCLEUS; EUKARYOTE; FEEDBACK SYSTEM; GENE EXPRESSION; HUMAN; NONHUMAN; NUCLEAR EXPORT SIGNAL; PRIORITY JOURNAL; PROKARYOTE; QUALITY CONTROL; REVIEW;

ACTIVE TRANSPORT, CELL NUCLEUS; DNA, INTERGENIC; EUKARYOTIC CELLS; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; INTRONS; OPEN READING FRAMES; RNA TRANSPORT; RNA, MESSENGER; RNA, UNTRANSLATED; TRANSCRIPTION INITIATION SITE;

EUKARYOTA; VERTEBRATA;

EID: 84860431158     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2011.12.012     Document Type: Review

References (203)

1. Gregory T.R. Synergy between sequence and size in large-scale genomics. Nat. Rev. Genet. 2005, 6:699-708.
2. Lynch M., Bobay L.-M., Catania F., Gout J.-F., Rho M. The repatterning of eukaryotic genomes by random genetic drift. Annu. Rev. Genomics Hum. Genet. 2011, 12:347-366.
3. Lynch M. The Origins of Genome Architecture 2007, Sinauer Associates, Sunderland Mass.
4. Lynch M. Streamlining and simplification of microbial genome architecture. Annu. Rev. Microbiol. 2006, 60:327-349.
5. Taft R.J., Pheasant M., Mattick J.S. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007, 29:288-299.
6. Mattick J.S., Taft R.J., Faulkner G.J. A global view of genomic information-moving beyond the gene and the master regulator. Trends Genet. 2010, 26:21-28.
7. Johnson J.M., Edwards S., Shoemaker D., Schadt E.E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 2005, 21:93-102.
8. Birney E., Stamatoyannopoulos J.A., Dutta A., Guigó R., Gingeras T.R., Margulies E.H., Weng Z., Snyder M., Dermitzakis E.T., Thurman R.E., Kuehn M.S., Taylor C.M., Neph S., Koch C.M., Asthana S., Malhotra A., Adzhubei I., Greenbaum J.A., Andrews R.M., Flicek P., Boyle P.J., Cao H., Carter N.P., Clelland G.K., Davis S., Day N., Dhami P., Dillon S.C., Dorschner M.O., Fiegler H., Giresi P.G., Goldy J., Hawrylycz M., Haydock A., Humbert R., James K.D., Johnson B.E., Johnson E.M., Frum T.T., Rosenzweig E.R., Karnani N., Lee K., Lefebvre G.C., Navas P.A., Neri F., Parker S.C.J., Sabo P.J., Sandstrom R., Shafer A., Vetrie D., Weaver M., Wilcox S., Yu M., Collins F.S., Dekker J., Lieb J.D., Tullius T.D., Crawford G.E., Sunyaev S., Noble W.S., Dunham I., Denoeud F., Reymond A., Kapranov P., Rozowsky J., Zheng D., Castelo R., Frankish A., Harrow J., Ghosh S., Sandelin A., Hofacker I.L., Baertsch R., Keefe D., Dike S., Cheng J., Hirsch H.A., Sekinger E.A., Lagarde J., Abril J.F., Shahab A., Flamm C., Fried C., Hackermüller J., Hertel J., Lindemeyer M., Missal K., Tanzer A., Washietl S., Korbel J., Emanuelsson O., Pedersen J.S., Holroyd N., Taylor R., Swarbreck D., Matthews N., Dickson M.C., Thomas D.J., Weirauch M.T., Gilbert J., Drenkow J., Bell I., Zhao X., Srinivasan K.G., Sung W.-K., Ooi H.S., Chiu K.P., Foissac S., Alioto T., Brent M., Pachter L., Tress M.L., Valencia A., Choo S.W., Choo C.Y., Ucla C., Manzano C., Wyss C., Cheung E., Clark T.G., Brown J.B., Ganesh M., Patel S., Tammana H., Chrast J., Henrichsen C.N., Kai C., Kawai J., Nagalakshmi U., Wu J., Lian Z., Lian J., Newburger P., Zhang X., Bickel P., Mattick J.S., Carninci P., Hayashizaki Y., Weissman S., Hubbard T., Myers R.M., Rogers J., Stadler P.F., Lowe T.M., Wei C.-L., Ruan Y., Struhl K., Gerstein M., Antonarakis S.E., Fu Y., Green E.D., Karaöz U., Siepel A., Taylor J., Liefer L.A., Wetterstrand K.A., Good P.J., Feingold E.A., Guyer M.S., Cooper G.M., Asimenos G., Dewey C.N., Hou M., Nikolaev S., Montoya-Burgos J.I., Löytynoja A., Whelan S., Pardi F., Massingham T., Huang H., Zhang N.R., Holmes I., Mullikin J.C., Ureta-Vidal A., Paten B., Seringhaus M., Church D., Rosenbloom K., Kent W.J., Stone E.A., Batzoglou S., Goldman N., Hardison R.C., Haussler D., Miller W., Sidow A., Trinklein N.D., Zhang Z.D., Barrera L., Stuart R., King D.C., Ameur A., Enroth S., Bieda M.C., Kim J., Bhinge A.A., Jiang N., Liu J., Yao F., Vega V.B., Lee C.W.H., Ng P., Shahab A., Yang A., Moqtaderi Z., Zhu Z., Xu X., Squazzo S., Oberley M.J., Inman D., Singer M.A., Richmond T.A., Munn K.J., Rada-Iglesias A., Wallerman O., Komorowski J., Fowler J.C., Couttet P., Bruce A.W., Dovey O.M., Ellis P.D., Langford C.F., Nix D.A., Euskirchen G., Hartman S., Urban A.E., Kraus P., Van Calcar S., Heintzman N., Kim T.H., Wang K., Qu C., Hon G., Luna R., Glass C.K., Rosenfeld M.G., Aldred S.F., Cooper S.J., Halees A., Lin J.M., Shulha H.P., Zhang X., Xu M., Haidar J.N.S., Yu Y., Ruan Y., Iyer V.R., Green R.D., Wadelius C., Farnham P.J., Ren B., Harte R.A., Hinrichs A.S., Trumbower H., Clawson H., Hillman-Jackson J., Zweig A.S., Smith K., Thakkapallayil A., Barber G., Kuhn R.M., Karolchik D., Armengol L., Bird C.P., de Bakker P.I.W., Kern A.D., Lopez-Bigas N., Martin J.D., Stranger B.E., Woodroffe A., Davydov E., Dimas A., Eyras E., Hallgrímsdóttir I.B., Huppert J., Zody M.C., Abecasis G.R., Estivill X., Bouffard G.G., Guan X., Hansen N.F., Idol J.R., Maduro V.V.B., Maskeri B., McDowell J.C., Park M., Thomas P.J., Young A.C., Blakesley R.W., Muzny D.M., Sodergren E., Wheeler D.A., Worley K.C., Jiang H., Weinstock G.M., Gibbs R.A., Graves T., Fulton R., Mardis E.R., Wilson R.K., Clamp M., Cuff J., Gnerre S., Jaffe D.B., Chang J.L., Lindblad-Toh K., Lander E.S., Koriabine M., Nefedov M., Osoegawa K., Yoshinaga Y., Zhu B., de Jong P.J. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
9. Wang J., Zhang J., Zheng H., Li J., Liu D., Li H., Samudrala R., Yu J., Wong G.K.-S. Mouse transcriptome: neutral evolution of "non-coding" complementary DNAs. Nature 2004, 431. 1 p following 757; discussion following 757.
10. Marques A.C., Ponting C.P. Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol. 2009, 10:R124.
11. Wyers F., Rougemaille M., Badis G., Rousselle J.-C., Dufour M.-E., Boulay J., Régnault B., Devaux F., Namane A., Séraphin B., Libri D., Jacquier A. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 2005, 121:725-737.
12. Thiebaut M., Kisseleva-Romanova E., Rougemaille M., Boulay J., Libri D. Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol. Cell 2006, 23:853-864.
13. Davis C.A., Ares M. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:3262-3267.
14. Chekanova J.A., Gregory B.D., Reverdatto S.V., Chen H., Kumar R., Hooker T., Yazaki J., Li P., Skiba N., Peng Q., Alonso J., Brukhin V., Grossniklaus U., Ecker J.R., Belostotsky D.A. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 2007, 131:1340-1353.
15. Vasiljeva L., Kim M., Terzi N., Soares L.M., Buratowski S. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol. Cell 2008, 29:313-323.
16. Preker P., Nielsen J., Kammler S., Lykke-Andersen S., Christensen M.S., Mapendano C.K., Schierup M.H., Jensen T.H. RNA exosome depletion reveals transcription upstream of active human promoters. Science 2008, 322:1851-1854.
17. Neil H., Malabat C., d' Aubenton-Carafa Y., Xu Z., Steinmetz L.M., Jacquier A. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 2009, 457:1038-1042.
18. Xu Z., Wei W., Gagneur J., Perocchi F., Clauder-Münster S., Camblong J., Guffanti E., Stutz F., Huber W., Steinmetz L.M. Bidirectional promoters generate pervasive transcription in yeast. Nature 2009, 457:1033-1037.
19. Babak T., Blencowe B.J., Hughes T.R. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics 2005, 6:104.
20. van Bakel H., Nislow C., Blencowe B.J., Hughes T.R. Most "dark matter" transcripts are associated with known genes. PLoS Biol. 2010, 8:e1000371.
21. Martens J.A., Laprade L., Winston F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 2004, 429:571-574.
22. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811.
23. Tsai M.-C., Manor O., Wan Y., Mosammaparast N., Wang J.K., Lan F., Shi Y., Segal E., Chang H.Y. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010, 329:689-693.
24. Bartolomei M.S., Zemel S., Tilghman S.M. Parental imprinting of the mouse H19 gene. Nature 1991, 351:153-155.
25. Kobayashi T., Ganley A.R.D. Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science 2005, 309:1581-1584.
26. Salmena L., Poliseno L., Tay Y., Kats L., Pandolfi P.P. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?. Cell 2011, 146:353-358.
27. Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser D., Huarte M., Zuk O., Carey B.W., Cassady J.P., Cabili M.N., Jaenisch R., Mikkelsen T.S., Jacks T., Hacohen N., Bernstein B.E., Kellis M., Regev A., Rinn J.L., Lander E.S. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458:223-227.
28. Guttman M., Garber M., Levin J.Z., Donaghey J., Robinson J., Adiconis X., Fan L., Koziol M.J., Gnirke A., Nusbaum C., Rinn J.L., Lander E.S., Regev A. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 2010, 28:503-510.
29. Managadze D., Rogozin I.B., Chernikova D., Shabalina S.A., Koonin E.V. Negative correlation between expression level and evolutionary rate of long intergenic non-coding RNAs. Genome Biol. Evol. 2011, 3:1390-1404.
30. Rogozin I.B., Wolf Y.I., Sorokin A.V., Mirkin B.G., Koonin E.V. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol. 2003, 13:1512-1517.
31. Irimia M., Penny D., Roy S.W. Coevolution of genomic intron number and splice sites. Trends Genet. 2007, 23:321-325.
32. Irimia M., Roy S.W. Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome. PLoS Genet. 2008, 4:e1000148.
33. Csuros M., Rogozin I.B., Koonin E.V. A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comput. Biol. 2011, 7:e1002150.
34. Koonin E. The Logic of Chance: the Nature and Origin of Biological Evolution 2011, Pearson Education, Upper Saddle River N.J.
35. Kuo C.-H., Ochman H. Deletional bias across the three domains of life. Genome Biol. Evol. 2009, 1:145-152.
36. Chen W.-H., Wei W., Lercher M.J. Minimal regulatory spaces in yeast genomes. BMC Genomics 2011, 12:320.
37. Lynch M., Scofield D.G., Hong X. The evolution of transcription-initiation sites. Mol. Biol. Evol. 2005, 22:1137-1146.
38. Hahn M.W., Stajich J.E., Wray G.A. The effects of selection against spurious transcription factor binding sites. Mol. Biol. Evol. 2003, 20:901-906.
39. Froula J.L., Francino M.P. Selection against spurious promoter motifs correlates with translational efficiency across bacteria. PLoS One 2007, 2:e745.
40. Carninci P., Sandelin A., Lenhard B., Katayama S., Shimokawa K., Ponjavic J., Semple C.A.M., Taylor M.S., Engström P.G., Frith M.C., Forrest A.R.R., Alkema W.B., Tan S.L., Plessy C., Kodzius R., Ravasi T., Kasukawa T., Fukuda S., Kanamori-Katayama M., Kitazume Y., Kawaji H., Kai C., Nakamura M., Konno H., Nakano K., Mottagui-Tabar S., Arner P., Chesi A., Gustincich S., Persichetti F., Suzuki H., Grimmond S.M., Wells C.A., Orlando V., Wahlestedt C., Liu E.T., Harbers M., Kawai J., Bajic V.B., Hume D.A., Hayashizaki Y. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 2006, 38:626-635.
41. Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R.R., Zavolan M., Davis M.J., Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P.T., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schönbach C., Sekiguchi K., Semple C.A.M., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563.
42. Cheung V., Chua G., Batada N.N., Landry C.R., Michnick S.W., Hughes T.R., Winston F. Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol. 2008, 6:e277.
43. Buratowski S. Transcription. Gene expression-where to start?. Science 2008, 322:1804-1805.
44. Steinmetz E.J., Warren C.L., Kuehner J.N., Panbehi B., Ansari A.Z., Brow D.A. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol. Cell 2006, 24:735-746.
45. Struhl K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat. Struct. Mol. Biol. 2007, 14:103-105.
46. Maniatis T., Reed R. An extensive network of coupling among gene expression machines. Nature 2002, 416:499-506.
47. Moore M.J., Proudfoot N.J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 2009, 136:688-700.
48. Perales R., Bentley D. "Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions. Mol. Cell 2009, 36:178-191.
49. Hocine S., Singer R.H., Grünwald D. RNA processing and export. Cold Spring Harb. Perspect. Biol. 2010, 2:a000752.
50. Ohno M., Segref A., Kuersten S., Mattaj I.W. Identity elements used in export of mRNAs. Mol. Cell 2002, 9:659-671.
51. Ullman K.S. RNA export: searching for mRNA identity. Curr. Biol. 2002, 12:R461-R463.
52. Masuyama K., Taniguchi I., Kataoka N., Ohno M. RNA length defines RNA export pathway. Genes Dev. 2004, 18:2074-2085.
53. Fuke H., Ohno M. Role of poly (A) tail as an identity element for mRNA nuclear export. Nucleic Acids Res. 2008, 36:1037-1049.
54. Martin W., Koonin E.V. Introns and the origin of nucleus-cytosol compartmentalization. Nature 2006, 440:41-45.
55. Chávez S., Beilharz T., Rondón A.G., Erdjument-Bromage H., Tempst P., Svejstrup J.Q., Lithgow T., Aguilera A. A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae. EMBO J. 2000, 19:5824-5834.
56. Strässer K., Masuda S., Mason P., Pfannstiel J., Oppizzi M., Rodriguez-Navarro S., Rondón A.G., Aguilera A., Struhl K., Reed R., Hurt E. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 2002, 417:304-308.
57. Strässer K., Hurt E. Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p. Nature 2001, 413:648-652.
58. Jimeno S., Rondón A.G., Luna R., Aguilera A. The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instability. EMBO J. 2002, 21:3526-3535.
59. Zenklusen D., Vinciguerra P., Wyss J.-C., Stutz F. Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol. Cell. Biol. 2002, 22:8241-8253.
60. Rehwinkel J., Herold A., Gari K., Köcher T., Rode M., Ciccarelli F.L., Wilm M., Izaurralde E. Genome-wide analysis of mRNAs regulated by the THO complex in Drosophila melanogaster. Nat. Struct. Mol. Biol. 2004, 11:558-566.
61. Masuda S., Das R., Cheng H., Hurt E., Dorman N., Reed R. Recruitment of the human TREX complex to mRNA during splicing. Genes Dev. 2005, 19:1512-1517.
62. Kapadia F., Pryor A., Chang T.-H., Johnson L.F. Nuclear localization of poly(A)+ mRNA following siRNA reduction of expression of the mammalian RNA helicases UAP56 and URH49. Gene 2006, 384:37-44.
63. Luo M.L., Zhou Z., Magni K., Christoforides C., Rappsilber J., Mann M., Reed R. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly. Nature 2001, 413:644-647.
64. Kota K.P., Wagner S.R., Huerta E., Underwood J.M., Nickerson J.A. Binding of ATP to UAP56 is necessary for mRNA export. J. Cell Sci. 2008, 121:1526-1537.
65. Dias A.P., Dufu K., Lei H., Reed R. A role for TREX components in the release of spliced mRNA from nuclear speckle domains. Nat. Commun. 2010, 1:97.
66. Spector D.L., Lamond A.I. Nuclear speckles. Cold Spring Harb. Perspect. Biol. 2011, 3.
67. Taniguchi I., Ohno M. ATP-dependent recruitment of export factor Aly/REF onto intronless mRNAs by RNA helicase UAP56. Mol. Cell. Biol. 2008, 28:601-608.
68. Dufu K., Livingstone M.J., Seebacher J., Gygi S.P., Wilson S.A., Reed R. ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. Genes Dev. 2010, 24:2043-2053.
69. Strässer K., Hurt E. Yra1p, a conserved nuclear RNA-binding protein, interacts directly with Mex67p and is required for mRNA export. EMBO J. 2000, 19:410-420.
70. Stutz F., Bachi A., Doerks T., Braun I.C., Séraphin B., Wilm M., Bork P., Izaurralde E. REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. RNA 2000, 6:638-650.
71. Hautbergue G.M., Hung M.-L., Golovanov A.P., Lian L.-Y., Wilson S.A. Mutually exclusive interactions drive handover of mRNA from export adaptors to TAP. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:5154-5159.
72. Schmidt U., Richter K., Berger A.B., Lichter P. In vivo BiFC analysis of Y14 and NXF1 mRNA export complexes: preferential localization within and around SC35 domains. J. Cell Biol. 2006, 172:373-381.
73. Segref A., Sharma K., Doye V., Hellwig A., Huber J., Lührmann R., Hurt E. Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. EMBO J. 1997, 16:3256-3271.
74. Katahira J., Strässer K., Podtelejnikov A., Mann M., Jung J.U., Hurt E. The Mex67p-mediated nuclear mRNA export pathway is conserved from yeast to human. EMBO J. 1999, 18:2593-2609.
75. Santos-Rosa H., Moreno H., Simos G., Segref A., Fahrenkrog B., Panté N., Hurt E. Nuclear mRNA export requires complex formation between Mex67p and Mtr2p at the nuclear pores. Mol. Cell. Biol. 1998, 18:6826-6838.
76. Hobeika M., Brockmann C., Iglesias N., Gwizdek C., Neuhaus D., Stutz F., Stewart M., Divita G., Dargemont C. Coordination of Hpr1 and ubiquitin binding by the UBA domain of the mRNA export factor Mex67. Mol. Biol. Cell 2007, 18:2561-2568.
77. Thakurta A.G., Gopal G., Yoon J.H., Kozak L., Dhar R. Homolog of BRCA2-interacting Dss1p and Uap56p link Mlo3p and Rae1p for mRNA export in fission yeast. EMBO J. 2005, 24:2512-2523.
78. Thakurta A.G., Selvanathan S.P., Patterson A.D., Gopal G., Dhar R. The nuclear export signal of splicing factor Uap56p interacts with nuclear pore-associated protein Rae1p for mRNA export in Schizosaccharomyces pombe. J. Biol. Chem. 2007, 282:17507-17516.
79. Bailer S.M., Siniossoglou S., Podtelejnikov A., Hellwig A., Mann M., Hurt E. Nup116p and nup100p are interchangeable through a conserved motif which constitutes a docking site for the mRNA transport factor gle2p. EMBO J. 1998, 17:1107-1119.
80. Pritchard C.E., Fornerod M., Kasper L.H., van Deursen J.M. RAE1 is a shuttling mRNA export factor that binds to a GLEBS-like NUP98 motif at the nuclear pore complex through multiple domains. J. Cell Biol. 1999, 145:237-254.
81. Yoon J.H., Love D.C., Guhathakurta A., Hanover J.A., Dhar R. Mex67p of Schizosaccharomyces pombe interacts with Rae1p in mediating mRNA export. Mol. Cell. Biol. 2000, 20:8767-8782.
82. Blevins M.B., Smith A.M., Phillips E.M., Powers M.A. Complex formation among the RNA export proteins Nup98, Rae1/Gle2, and TAP. J. Biol. Chem. 2003, 278:20979-20988.
83. Weirich C.S., Erzberger J.P., Flick J.S., Berger J.M., Thorner J., Weis K. Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export. Nat. Cell Biol. 2006, 8:668-676.
84. Alcázar-Román A.R., Tran E.J., Guo S., Wente S.R. Inositol hexakisphosphate and Gle1 activate the DEAD-box protein Dbp5 for nuclear mRNA export. Nat. Cell Biol. 2006, 8:711-716.
85. Lund M.K., Guthrie C. The DEAD-box protein Dbp5p is required to dissociate Mex67p from exported mRNPs at the nuclear rim. Mol. Cell 2005, 20:645-651.
86. Schmitt C., von Kobbe C., Bachi A., Panté N., Rodrigues J.P., Boscheron C., Rigaut G., Wilm M., Séraphin B., Carmo-Fonseca M., Izaurralde E. Dbp5, a DEAD-box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p. EMBO J. 1999, 18:4332-4347.
87. Hodge C.A., Colot H.V., Stafford P., Cole C.N. Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells. EMBO J. 1999, 18:5778-5788.
88. Zhou Z., Luo M.J., Straesser K., Katahira J., Hurt E., Reed R. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature 2000, 407:401-405.
89. Meignin C., Davis I. UAP56 RNA helicase is required for axis specification and cytoplasmic mRNA localization in Drosophila. Dev. Biol. 2008, 315:89-98.
90. Katahira J., Inoue H., Hurt E., Yoneda Y. Adaptor Aly and co-adaptor Thoc5 function in the Tap-p15-mediated nuclear export of HSP70 mRNA. EMBO J. 2009, 28:556-567.
91. Thomas M., Lischka P., Müller R., Stamminger T. The cellular DExD/H-Box RNA-helicases UAP56 and URH49 exhibit a CRM1-independent nucleocytoplasmic shuttling activity. PLoS One 2011, 6:e22671.
92. Long J.C., Caceres J.F. The SR protein family of splicing factors: master regulators of gene expression. Biochem. J. 2009, 417:15-27.
93. Hurt E., Luo M.-J., Röther S., Reed R., Strässer K. Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:1858-1862.
94. Huang Y., Steitz J.A. Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA. Mol. Cell 2001, 7:899-905.
95. Huang Y., Gattoni R., Stévenin J., Steitz J.A. SR splicing factors serve as adapter proteins for TAP-dependent mRNA export. Mol. Cell 2003, 11:837-843.
96. Cáceres J.F., Screaton G.R., Krainer A.R. A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. Genes Dev. 1998, 12:55-66.
97. Buratowski S. Progression through the RNA polymerase II CTD cycle. Mol. Cell 2009, 36:541-546.
98. Feaver W.J., Svejstrup J.Q., Henry N.L., Kornberg R.D. Relationship of CDK-activating kinase and RNA polymerase II CTD kinase TFIIH/TFIIK. Cell 1994, 79:1103-1109.
99. Cho E.J., Takagi T., Moore C.R., Buratowski S. mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. 1997, 11:3319-3326.
100. McCracken S., Fong N., Rosonina E., Yankulov K., Brothers G., Siderovski D., Hessel A., Foster S., Shuman S., Bentley D.L. 5'-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev. 1997, 11:3306-3318.
101. Yue Z., Maldonado E., Pillutla R., Cho H., Reinberg D., Shatkin A.J. Mammalian capping enzyme complements mutant Saccharomyces cerevisiae lacking mRNA guanylyltransferase and selectively binds the elongating form of RNA polymerase II. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:12898-12903.
102. Cheng H., Dufu K., Lee C.-S., Hsu J.L., Dias A., Reed R. Human mRNA export machinery recruited to the 5' end of mRNA. Cell 2006, 127:1389-1400.
103. Zhao J., Jin S.-B., Björkroth B., Wieslander L., Daneholt B. The mRNA export factor Dbp5 is associated with Balbiani ring mRNP from gene to cytoplasm. EMBO J. 2002, 21:1177-1187.
104. Estruch F., Cole C.N. An early function during transcription for the yeast mRNA export factor Dbp5p/Rat8p suggested by its genetic and physical interactions with transcription factor IIH components. Mol. Biol. Cell 2003, 14:1664-1676.
105. Blobel G. Gene gating: a hypothesis. Proc. Natl. Acad. Sci. U. S. A. 1985, 82:8527-8529.
106. Casolari J.M., Brown C.R., Komili S., West J., Hieronymus H., Silver P.A. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 2004, 117:427-439.
107. Kurshakova M.M., Krasnov A.N., Kopytova D.V., Shidlovskii Y.V., Nikolenko J.V., Nabirochkina E.N., Spehner D., Schultz P., Tora L., Georgieva S.G. SAGA and a novel Drosophila export complex anchor efficient transcription and mRNA export to NPC. EMBO J. 2007, 26:4956-4965.
108. Brickner J.H. Transcriptional memory at the nuclear periphery. Curr. Opin. Cell Biol. 2009, 21:127-133.
109. Fischer T., Strässer K., Rácz A., Rodriguez-Navarro S., Oppizzi M., Ihrig P., Lechner J., Hurt E. The mRNA export machinery requires the novel Sac3p-Thp1p complex to dock at the nucleoplasmic entrance of the nuclear pores. EMBO J. 2002, 21:5843-5852.
110. Cabal G.G., Genovesio A., Rodriguez-Navarro S., Zimmer C., Gadal O., Lesne A., Buc H., Feuerbach-Fournier F., Olivo-Marin J.-C., Hurt E.C., Nehrbass U. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 2006, 441:770-773.
111. Luthra R., Kerr S.C., Harreman M.T., Apponi L.H., Fasken M.B., Ramineni S., Chaurasia S., Valentini S.R., Corbett A.H. Actively transcribed GAL genes can be physically linked to the nuclear pore by the SAGA chromatin modifying complex. J. Biol. Chem. 2007, 282:3042-3049.
112. Fischer T., Rodríguez-Navarro S., Pereira G., Rácz A., Schiebel E., Hurt E. Yeast centrin Cdc31 is linked to the nuclear mRNA export machinery. Nat. Cell Biol. 2004, 6:840-848.
113. Lei E.P., Stern C.A., Fahrenkrog B., Krebber H., Moy T.I., Aebi U., Silver P.A. Sac3 is an mRNA export factor that localizes to cytoplasmic fibrils of nuclear pore complex. Mol. Biol. Cell 2003, 14:836-847.
114. Rodríguez-Navarro S., Fischer T., Luo M.-J., Antúnez O., Brettschneider S., Lechner J., Pérez-Ortín J.E., Reed R., Hurt E. Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery. Cell 2004, 116:75-86.
115. Jani D., Lutz S., Marshall N.J., Fischer T., Köhler A., Ellisdon A.M., Hurt E., Stewart M. Sus1, Cdc31, and the Sac3 CID region form a conserved interaction platform that promotes nuclear pore association and mRNA export. Mol. Cell 2009, 33:727-737.
116. Wickramasinghe V.O., McMurtrie P.I.A., Mills A.D., Takei Y., Penrhyn-Lowe S., Amagase Y., Main S., Marr J., Stewart M., Laskey R.A. mRNA export from mammalian cell nuclei is dependent on GANP. Curr. Biol. 2010, 20:25-31.
117. Svejstrup J.Q. The RNA polymerase II transcription cycle: cycling through chromatin. Biochim. Biophys. Acta 2004, 1677:64-73.
118. Bartkowiak B., Greenleaf A.L. Phosphorylation of RNAPII: to P-TEFb or not to P-TEFb?. Transcription 2011, 2:115-119.
119. Lenasi T., Barboric M. P-TEFb stimulates transcription elongation and pre-mRNA splicing through multilateral mechanisms. RNA Biol. 2010, 7:145-150.
120. Mackellar A.L., Greenleaf A.L. Cotranscriptional association of mRNA export factor Yra1 with the C-terminal domain of RNA polymerase II: a mechanism for cotranscriptional recruitment. J. Biol. Chem. 2011, 286:36385-36395.
121. Chang M., French-Cornay D., Fan H.Y., Klein H., Denis C.L., Jaehning J.A. A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol. Cell. Biol. 1999, 19:1056-1067.
122. Kopytova D.V., Orlova A.V., Krasnov A.N., Gurskiy D.Y., Nikolenko J.V., Nabirochkina E.N., Shidlovskii Y.V., Georgieva S.G. Multifunctional factor ENY2 is associated with the THO complex and promotes its recruitment onto nascent mRNA. Genes Dev. 2010, 24:86-96.
123. Chávez S., García-Rubio M., Prado F., Aguilera A. Hpr1 is preferentially required for transcription of either long or G+C-rich DNA sequences in Saccharomyces cerevisiae. Mol. Cell. Biol. 2001, 21:7054-7064.
124. Li Y., Wang X., Zhang X., Goodrich D.W. Human hHpr1/p84/Thoc1 regulates transcriptional elongation and physically links RNA polymerase II and RNA processing factors. Mol. Cell. Biol. 2005, 25:4023-4033.
125. Belotserkovskaya R., Reinberg D. Facts about FACT and transcript elongation through chromatin. Curr. Opin. Genet. Dev. 2004, 14:139-146.
126. Yoh S.M., Cho H., Pickle L., Evans R.M., Jones K.A. The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. Genes Dev. 2007, 21:160-174.
127. Kaplan C.D., Laprade L., Winston F. Transcription elongation factors repress transcription initiation from cryptic sites. Science 2003, 301:1096-1099.
128. Mason P.B., Struhl K. The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol. Cell. Biol. 2003, 23:8323-8333.
129. Yoh S.M., Lucas J.S., Jones K.A. The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. Genes Dev. 2008, 22:3422-3434.
130. Hautbergue G.M., Hung M.-L., Walsh M.J., Snijders A.P.L., Chang C.-T., Jones R., Ponting C.P., Dickman M.J., Wilson S.A. UIF, a new mRNA export adaptor that works together with REF/ALY, requires FACT for recruitment to mRNA. Curr. Biol. 2009, 19:1918-1924.
131. Parenteau J., Durand M., Véronneau S., Lacombe A.-A., Morin G., Guérin V., Cecez B., Gervais-Bird J., Koh C.-S., Brunelle D., Wellinger R.J., Chabot B., Abou Elela S. Deletion of many yeast introns reveals a minority of genes that require splicing for function. Mol. Biol. Cell 2008, 19:1932-1941.
132. Juneau K., Miranda M., Hillenmeyer M.E., Nislow C., Davis R.W. Introns regulate RNA and protein abundance in yeast. Genetics 2006, 174:511-518.
133. Parenteau J., Durand M., Morin G., Gagnon J., Lucier J.-F., Wellinger R.J., Chabot B., Elela S.A. Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell 2011, 147:320-331.
134. McCracken S., Lambermon M., Blencowe B.J. SRm160 splicing coactivator promotes transcript 3'-end cleavage. Mol. Cell. Biol. 2002, 22:148-160.
135. Lutz C.S., Murthy K.G., Schek N., O'Connor J.P., Manley J.L., Alwine J.C. Interaction between the U1 snRNP-A protein and the 160-kD subunit of cleavage-polyadenylation specificity factor increases polyadenylation efficiency in vitro. Genes Dev. 1996, 10:325-337.
136. Luo M.J., Reed R. Splicing is required for rapid and efficient mRNA export in metazoans. Proc. Natl. Acad. Sci. U. S. A. 1999, 96:14937-14942.
137. Fleckner J., Zhang M., Valcárcel J., Green M.R. U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. Genes Dev. 1997, 11:1864-1872.
138. Shen H. UAP56 - a key player with surprisingly diverse roles in pre-mRNA splicing and nuclear export. BMB Rep. 2009, 42:185-188.
139. Palazzo A.F., Springer M., Shibata Y., Lee C.-S., Dias A.P., Rapoport T.A. The signal sequence coding region promotes nuclear export of mRNA. PLoS Biol. 2007, 5:e322.
140. Le Hir H., Gatfield D., Izaurralde E., Moore M.J. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 2001, 20:4987-4997.
141. Giorgi C., Yeo G.W., Stone M.E., Katz D.B., Burge C., Turrigiano G., Moore M.J. The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell 2007, 130:179-191.
142. Nott A., Le Hir H., Moore M.J. Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev. 2004, 18:210-222.
143. Ma X.M., Yoon S.-O., Richardson C.J., Jülich K., Blenis J. SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs. Cell 2008, 133:303-313.
144. Le Hir H., Gatfield D., Braun I.C., Forler D., Izaurralde E. The protein Mago provides a link between splicing and mRNA localization. EMBO Rep. 2001, 2:1119-1124.
145. Hachet O., Ephrussi A. Drosophila Y14 shuttles to the posterior of the oocyte and is required for oskar mRNA transport. Curr. Biol. 2001, 11:1666-1674.
146. Hachet O., Ephrussi A. Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization. Nature 2004, 428:959-963.
147. Kim M., Ahn S.-H., Krogan N.J., Greenblatt J.F., Buratowski S. Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. EMBO J. 2004, 23:354-364.
148. Lei E.P., Silver P.A. Intron status and 3'-end formation control cotranscriptional export of mRNA. Genes Dev. 2002, 16:2761-2766.
149. Johnson S.A., Cubberley G., Bentley D.L. Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3' end processing factor Pcf11. Mol. Cell 2009, 33:215-226.
150. Rougemaille M., Dieppois G., Kisseleva-Romanova E., Gudipati R.K., Lemoine S., Blugeon C., Boulay J., Jensen T.H., Stutz F., Devaux F., Libri D. THO/Sub2p functions to coordinate 3'-end processing with gene-nuclear pore association. Cell 2008, 135:308-321.
151. Libri D., Dower K., Boulay J., Thomsen R., Rosbash M., Jensen T.H. Interactions between mRNA export commitment, 3'-end quality control, and nuclear degradation. Mol. Cell. Biol. 2002, 22:8254-8266.
152. Saguez C., Schmid M., Olesen J.R., Ghazy M.A.E.-H., Qu X., Poulsen M.B., Nasser T., Moore C., Jensen T.H. Nuclear mRNA surveillance in THO/sub2 mutants is triggered by inefficient polyadenylation. Mol. Cell 2008, 31:91-103.
153. Farny N.G., Hurt J.A., Silver P.A. Definition of global and transcript-specific mRNA export pathways in metazoans. Genes Dev. 2008, 22:66-78.
154. Hector R.E., Nykamp K.R., Dheur S., Anderson J.T., Non P.J., Urbinati C.R., Wilson S.M., Minvielle-Sebastia L., Swanson M.S. Dual requirement for yeast hnRNP Nab2p in mRNA poly(A) tail length control and nuclear export. EMBO J. 2002, 21:1800-1810.
155. Green D.M., Marfatia K.A., Crafton E.B., Zhang X., Cheng X., Corbett A.H. Nab2p is required for poly(A) RNA export in Saccharomyces cerevisiae and is regulated by arginine methylation via Hmt1p. J. Biol. Chem. 2002, 277:7752-7760.
156. Fasken M.B., Stewart M., Corbett A.H. Functional significance of the interaction between the mRNA-binding protein, Nab2, and the nuclear pore-associated protein, Mlp1, in mRNA export. J. Biol. Chem. 2008, 283:27130-27143.
157. Iglesias N., Tutucci E., Gwizdek C., Vinciguerra P., Von Dach E., Corbett A.H., Dargemont C., Stutz F. Ubiquitin-mediated mRNP dynamics and surveillance prior to budding yeast mRNA export. Genes Dev. 2010, 24:1927-1938.
158. Lainé J.-P., Singh B.N., Krishnamurthy S., Hampsey M. A physiological role for gene loops in yeast. Genes Dev. 2009, 23:2604-2609.
159. Rougemaille M., Gudipati R.K., Olesen J.R., Thomsen R., Seraphin B., Libri D., Jensen T.H. Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants. EMBO J. 2007, 26:2317-2326.
160. Assenholt J., Mouaikel J., Saguez C., Rougemaille M., Libri D., Jensen T.H. Implication of Ccr4-Not complex function in mRNA quality control in Saccharomyces cerevisiae. RNA 2011, 17:1788-1794.
161. Milligan L., Decourty L., Saveanu C., Rappsilber J., Ceulemans H., Jacquier A., Tollervey D. A yeast exosome cofactor, Mpp 6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts. Mol. Cell. Biol. 2008, 28:5446-5457.
162. Wilmes G.M., Bergkessel M., Bandyopadhyay S., Shales M., Braberg H., Cagney G., Collins S.R., Whitworth G.B., Kress T.L., Weissman J.S., Ideker T., Guthrie C., Krogan N.J. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol. Cell 2008, 32:735-746.
163. Kerr S.C., Azzouz N., Fuchs S.M., Collart M.A., Strahl B.D., Corbett A.H., Laribee R.N. The Ccr4-Not complex interacts with the mRNA export machinery. PLoS One 2011, 6:e18302.
164. Galy V., Gadal O., Fromont-Racine M., Romano A., Jacquier A., Nehrbass U. Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell 2004, 116:63-73.
165. Skruzný M., Schneider C., Rácz A., Weng J., Tollervey D., Hurt E. An endoribonuclease functionally linked to perinuclear mRNP quality control associates with the nuclear pore complexes. PLoS Biol. 2009, 7:e8.
166. Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature 2009, 457:413-420.
167. Zhang K., Fischer T., Porter R.L., Dhakshnamoorthy J., Zofall M., Zhou M., Veenstra T., Grewal S.I.S. Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA. Science 2011, 331:1624-1627.
168. Jauvion V., Elmayan T., Vaucheret H. The conserved RNA trafficking proteins HPR1 and TEX1 are involved in the production of endogenous and exogenous small interfering RNA in Arabidopsis. Plant Cell 2010, 22:2697-2709.
169. Yelina N.E., Smith L.M., Jones A.M.E., Patel K., Kelly K.A., Baulcombe D.C. Putative Arabidopsis THO/TREX mRNA export complex is involved in transgene and endogenous siRNA biosynthesis. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:13948-13953.
170. Fan H.Y., Merker R.J., Klein H.L. High-copy-number expression of Sub2p, a member of the RNA helicase superfamily, suppresses hpr1-mediated genomic instability. Mol. Cell. Biol. 2001, 21:5459-5470.
171. West R.W., Milgrom E. DEAD-box RNA helicase Sub2 is required for expression of lacZ fusions in Saccharomyces cerevisiae and is a dosage-dependent suppressor of RLR1 (THO2). Gene 2002, 288:19-27.
172. Lahue E., Heckathorn J., Meyer Z., Smith J., Wolfe C. The Saccharomyces cerevisiae Sub2 protein suppresses heterochromatic silencing at telomeres and subtelomeric genes. Yeast 2005, 22:537-551.
173. Eberl D.F., Lorenz L.J., Melnick M.B., Sood V., Lasko P., Perrimon N. A new enhancer of position-effect variegation in Drosophila melanogaster encodes a putative RNA helicase that binds chromosomes and is regulated by the cell cycle. Genetics 1997, 146:951-963.
174. Gross T., Siepmann A., Sturm D., Windgassen M., Scarcelli J.J., Seedorf M., Cole C.N., Krebber H. The DEAD-box RNA helicase Dbp5 functions in translation termination. Science 2007, 315:646-649.
175. Bolger T.A., Folkmann A.W., Tran E.J., Wente S.R. The mRNA export factor Gle1 and inositol hexakisphosphate regulate distinct stages of translation. Cell 2008, 134:624-633.
176. Alcázar-Román A.R., Bolger T.A., Wente S.R. Control of mRNA export and translation termination by inositol hexakisphosphate requires specific interaction with Gle1. J. Biol. Chem. 2010, 285:16683-16692.
177. Blobel G., Dobberstein B. Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma. J. Cell Biol. 1975, 67:835-851.
178. Cenik C., Chua H.N., Zhang H., Tarnawsky S., Akef A., Derti A., Tasan M., Moore M.J., Palazzo A.F., Roth F.P. Genome analysis reveals interplay between 5' UTR introns and nuclear mRNA export for secretory and mitochondrial genes. PLoS Genet. 2011, 7:e1001366.
179. Gueroussov S., Tarnawsky S.P., Cui X.A., Mahadevan K., Palazzo A.F. Analysis of mRNA nuclear export kinetics in mammalian cells by microinjection. J. Vis. Exp. 2010, 46:2387.
180. Kimura T., Hashimoto I., Nagase T., Fujisawa J.-I. CRM1-dependent, but not ARE-mediated, nuclear export of IFN-alpha1 mRNA. J. Cell Sci. 2004, 117:2259-2270.
181. Lei H., Dias A.P., Reed R. Export and stability of naturally intronless mRNAs require specific coding region sequences and the TREX mRNA export complex. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:17985-17990.
182. Williams E.J., Pal C., Hurst L.D. The molecular evolution of signal peptides. Gene 2000, 253:313-322.
183. Tordai H., Patthy L. Insertion of spliceosomal introns in proto-splice sites: the case of secretory signal peptides. FEBS Lett. 2004, 575:109-111.
184. von Heijne G. Mitochondrial targeting sequences may form amphiphilic helices. EMBO J. 1986, 5:1335-1342.
185. Roise D., Horvath S.J., Tomich J.M., Richards J.H., Schatz G. A chemically synthesized pre-sequence of an imported mitochondrial protein can form an amphiphilic helix and perturb natural and artificial phospholipid bilayers. EMBO J. 1986, 5:1327-1334.
186. Yu J., Hu S., Wang J., Wong G.K.-S., Li S., Liu B., Deng Y., Dai L., Zhou Y., Zhang X., Cao M., Liu J., Sun J., Tang J., Chen Y., Huang X., Lin W., Ye C., Tong W., Cong L., Geng J., Han Y., Li L., Li W., Hu G., Huang X., Li W., Li J., Liu Z., Li L., Liu J., Qi Q., Liu J., Li L., Li T., Wang X., Lu H., Wu T., Zhu M., Ni P., Han H., Dong W., Ren X., Feng X., Cui P., Li X., Wang H., Xu X., Zhai W., Xu Z., Zhang J., He S., Zhang J., Xu J., Zhang K., Zheng X., Dong J., Zeng W., Tao L., Ye J., Tan J., Ren X., Chen X., He J., Liu D., Tian W., Tian C., Xia H., Bao Q., Li G., Gao H., Cao T., Wang J., Zhao W., Li P., Chen W., Wang X., Zhang Y., Hu J., Wang J., Liu S., Yang J., Zhang G., Xiong Y., Li Z., Mao L., Zhou C., Zhu Z., Chen R., Hao B., Zheng W., Chen S., Guo W., Li G., Liu S., Tao M., Wang J., Zhu L., Yuan L., Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296:79-92.
187. Zhu L., Zhang Y., Zhang W., Yang S., Chen J.-Q., Tian D. Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMC Genomics 2009, 10:47.
188. Clay O., Cacciò S., Zoubak S., Mouchiroud D., Bernardi G. Human coding and noncoding DNA: compositional correlations. Mol. Phylogenet. Evol. 1996, 5:2-12.
189. Zhang L., Kasif S., Cantor C.R., Broude N.E. GC/AT-content spikes as genomic punctuation marks. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:16855-16860.
190. Kalari K.R., Casavant M., Bair T.B., Keen H.L., Comeron J.M., Casavant T.L., Scheetz T.E. First exons and introns-a survey of GC content and gene structure in the human genome. In Silico Biol. (Gedrukt) 2006, 6:237-242.
191. Xia X., Xie Z., Li W.-H. Effects of GC content and mutational pressure on the lengths of exons and coding sequences. J. Mol. Evol. 2003, 56:362-370.
192. Valencia P., Dias A.P., Reed R. Splicing promotes rapid and efficient mRNA export in mammalian cells. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:3386-3391.
193. Kimura T., Hashimoto I., Nishizawa M., Ito S., Yamada H. Novel cis-active structures in the coding region mediate CRM1-dependent nuclear export of IFN-α 1 mRNA. Med. Mol. Morphol. 2010, 43:145-157.
194. Prilusky J., Bibi E. Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:6662-6666.
195. Bibi E. Early targeting events during membrane protein biogenesis in Escherichia coli. Biochim. Biophys. Acta 2011, 1808:841-850.
196. Duret L., Galtier N. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu. Rev. Genomics Hum. Genet. 2009, 10:285-311.
197. Birdsell J.A. Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol. Biol. Evol. 2002, 19:1181-1197.
198. Gómez-González B., García-Rubio M., Bermejo R., Gaillard H., Shirahige K., Marín A., Foiani M., Aguilera A. Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles. EMBO J. 2011, 30:3106-3119.
199. González-Aguilera C., Tous C., Gómez-González B., Huertas P., Luna R., Aguilera A. The THP1-SAC3-SUS1-CDC31 complex works in transcription elongation-mRNA export preventing RNA-mediated genome instability. Mol. Biol. Cell 2008, 19:4310-4318.
200. Li X., Manley J.L. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 2005, 122:365-378.
201. Hieronymus H., Silver P.A. Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat. Genet. 2003, 33:155-161.
202. Kim Guisbert K., Duncan K., Li H., Guthrie C. Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles. RNA 2005, 11:383-393.
203. Lejeune F., Maquat L.E. Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr. Opin. Cell Biol. 2005, 17:309-315.