XIST RNA exhibits nuclear retention and exhibits reduced association with the export factor TAP/NXF1

Chromosoma

Volumn 116, Issue 4, 2007, Pages 373-383

  Cohen, Hannah R ^a,b   Panning, Barbara ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; EXPORT FACTOR TAP; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; UNCLASSIFIED DRUG; UNTRANSLATED RNA; X INACTIVE SPECIFIC TRANSCRIPT RNA;

ARTICLE; BINDING AFFINITY; BIOASSAY; CELL NUCLEUS; CELLULAR DISTRIBUTION; CHROMOSOME; CONTROLLED STUDY; CYTOPLASM; FEMALE; HETEROKARYON; HUMAN; HUMAN CELL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; WILD TYPE;

CELL LINE; CELL NUCLEUS; CHROMOSOMES, HUMAN; HUMANS; NUCLEOCYTOPLASMIC TRANSPORT PROTEINS; RNA, UNTRANSLATED; RNA-BINDING PROTEINS;

EID: 34347273047     PISSN: 00095915     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00412-007-0100-1     Document Type: Article

References (54)

1. Andersen AA, Panning B (2003) Epigenetic gene regulation by noncoding RNAs. Curr Opin Cell Biol 15:281-289
2. Andrulis ED, Werner J, Nazarian A, Erdjument-Bromage H, Tempst P, Lis JT (2002) The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature 420:837-841
3. Berk AJ, Sharp PA (1977) Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 12:721-732
4. Bernstein E, Allis CD (2005) RNA meets chromatin. Genes Dev 19:1635-1655
5. Brockdorff N, Ashworth A, Kay GF, McCabe VM, Norris DP, Cooper PJ, Swift S, Rastan S (1992) The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71:515-526
6. Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R, Willard HF (1991) A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349:38-44
7. Brown CJ, Hendrich BD, Rupert JL, Lafreniere RG, Xing Y, Lawrence J, Willard HF (1992) The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71:527-542
8. Buzin CH, Mann JR, Singer-Sam J (1994) Quantitative RT-PCR assays show Xist RNA levels are low in mouse female adult tissue, embryos and embryoid bodies. Development 120:3529-3536
9. Caceres JF, Screaton GR, Krainer AR (1998) A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. Genes Dev 12:55-66
10. Carmo-Fonseca M, Tollervey D, Pepperkok R, Barabino SM, Merdes A, Brunner C, Zamore PD, Green MR, Hurt E, Lamond AI (1991) Mammalian nuclei contain foci which are highly enriched in components of the pre-mRNA splicing machinery. EMBO J 10:195-206
11. Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL (2006) Mapping post-translational modifications of the histone variant macroH2A1 using tandem mass spectrometry. Mol Cell Proteomics 5:194-203
12. Clemson CM, McNeil JA, Willard HF, Lawrence JB (1996) XIST RNA paints the inactive X chromosome at interphase: Evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol 132:259-275
13. Clemson CM, Chow JC, Brown CJ, Lawrence JB (1998) Stabilization and localization of Xist RNA are controlled by separate mechanisms and are not sufficient for X inactivation. J Cell Biol 142:13-23
14. Clerc P, Avner P (1998) Role of the region 3′ to Xist exon 6 in the counting process of X-chromosome inactivation. Nat Genet 19:249-253
15. de Napoles M, Mermoud JE, Wakao R, Tang YA, Endoh M, Appanah R, Nesterova TB, Silva J, Otte AP, Vidal M et al (2004) Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev Cell 7:663-676
16. Dower K, Rosbash M (2002) T7 RNA polymerase-directed transcripts are processed in yeast and link 3′ end formation to mRNA nuclear export. RNA 8:686-697
17. Dower K, Kuperwasser N, Merrikh H, Rosbash M (2004) A synthetic A tail rescues yeast nuclear accumulation of a ribozyme-terminated transcript. RNA 10:1888-1899
18. Fang J, Chen T, Chadwick B, Li E, Zhang Y (2004) Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J Biol Chem 279:52812-52815
19. Femino AM, Fogarty K, Lifshitz LM, Carrington W, Singer RH (2003) Visualization of single molecules of mRNA in situ. Methods Enzymol 361:245-304
20. Fok V, Friend K, Steitz JA (2006) Epstein-Barr virus noncoding RNAs are confined to the nucleus, whereas their partner, the human La protein, undergoes nucleocytoplasmic shuttling. J Cell Biol 173:319-325
21. Hall LL, Byron M, Sakai K, Carrel L, Willard HF, Lawrence JB (2002) An ectopic human XIST gene can induce chromosome inactivation in postdifferentiation human HT-1080 cells. Proc Natl Acad Sci USA 99:8677-8682
22. Henry RA, Tews B, Li X, Scott MJ (2001) Recruitment of the male-specific lethal (MSL) dosage compensation complex to an autosomally integrated roX chromatin entry site correlates with an increased expression of an adjacent reporter gene in male Drosophila. J Biol Chem 276:31953-31958
23. Herold A, Teixeira L, Izaurralde E (2003) Genome-wide analysis of nuclear mRNA export pathways in Drosophila. EMBO J 22:2472-2483
24. Hilleren P, McCarthy T, Rosbash M, Parker R, Jensen TH (2001) Quality control of mRNA 3′-end processing is linked to the nuclear exosome. Nature 413:538-542
25. Hong YK, Ontiveros SD, Chen C, Strauss WM (1999) A new structure for the murine Xist gene and its relationship to chromosome choice/counting during X-chromosome inactivation. Proc Natl Acad Sci USA 96:6829-6834
26. Hong YK, Ontiveros SD, Strauss WM (2000) A revision of the human XIST gene organization and structural comparison with mouse Xist. Mamm Genome 11:220-224
27. Huang Y, Gattoni R, Stevenin J, Steitz JA (2003) SR splicing factors serve as adapter proteins for TAP-dependent mRNA export. Mol Cell 11:837-843
28. Huang Y, Yario TA, Steitz JA (2004) A molecular link between SR protein dephosphorylation and mRNA export. Proc Natl Acad Sci USA 101:9666-9670
29. Izaurralde E, Lewis J, Gamberi C, Jarmolowski A, McGuigan C, Mattaj IW (1995) A cap-binding protein complex mediating U snRNA export. Nature 376:709-712
30. Johnson CV, Singer RH, Lawrence JB (1991) Fluorescent detection of nuclear RNA and DNA: Implications for genome organization. Methods Cell Biol 35:73-99
31. Kageyama Y, Mengus G, Gilfillan G, Kennedy HG, Stuckenholz C, Kelley RL, Becker PB, Kuroda MI (2001) Association and spreading of the Drosophila dosage compensation complex from a discrete roX1 chromatin entry site. EMBO J 20:2236-2245
32. Kelley RL, Meller VH, Gordadze PR, Roman G, Davis RL, Kuroda MI (1999) Epigenetic spreading of the Drosophila dosage compensation complex from roX RNA genes into flanking chromatin. Cell 98:513-522
33. Lawrence JB, Singer RH (1985) Quantitative analysis of in situ hybridization methods for the detection of actin gene expression. Nucleic Acids Res 13:1777-1799
34. Lee JT, Jaenisch R (1997) Long-range cis effects of ectopic X-inactivation centres on a mouse autosome. Nature 386:275-279
35. Lyon MF (1961) Gene action in the X-chromosome of the mouse (Mus musculus L) Nature 190:372-373
36. Madore SJ, Wieben ED, Kunkel GR, Pederson T (1984) Precursors of U4 small nuclear RNA. J Cell Biol 99:1140-1144
37. Maquat LE (1995) When cells stop making sense: Effects of nonsense codons on RNA metabolism in vertebrate cells. RNA 1:453-465
38. Meller VH, Gordadze PR, Park Y, Chu X, Stuckenholz C, Kelley RL, Kuroda MI (2000) Ordered assembly of roX RNAs into MSL complexes on the dosage-compensated X chromosome in Drosophila. Curr Biol 10:136-143
39. Migeon BR, Winter H, Kazi E, Chowdhury AK, Hughes A, Haisley-Royster C, Morrison H, Jeppesen P (2001) Low-copy-number human transgene is recognized as an X inactivation center in mouse ES cells, but fails to induce cis-inactivation in chimeric mice. Genomics 71:156-162
40. Panning B (2004) X inactivation in mouse ES cells: Histone modifications and FISH. Methods Enzymol 376:419-428
41. Park Y, Kelley RL, Oh H, Kuroda MI, Meller VH (2002) Extent of chromatin spreading determined by roX RNA recruitment of MSL proteins. Science 298:1620-1623
42. Plath K, Mlynarczyk-Evans S, Nusinow DA, Panning B (2002) Xist RNA and the mechanism of X chromosome inactivation. Annu Rev Genet 36:233-278
43. Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300:131-135
44. Politz JC, Tuft RA, Pederson T, Singer RH (1999) Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr Biol 9:285-291
45. Rodrigues JP, Rode M, Gatfield D, Blencowe BJ, Carmo-Fonseca M, Izaurralde E (2001) REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus. Proc Natl Acad Sci USA 98:1030-1035
46. Seidl CI, Stricker SH, Barlow DP (2006) The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. Embo J 25:3565-3575
47. Schwartz RJ, Rothblum KN (1981) Gene switching in myogenesis: differential expression of the chicken actin multigene family. Biochemistry 20:4122-4129
48. Smith KP, Byron M, Clemson CM, Lawrence JB (2004) Ubiquitinated proteins including uH2A on the human and mouse inactive X chromosome: Enrichment in gene rich bands. Chromosoma 113:324-335
49. Stutz F, Bachi A, Doerks T, Braun IC, Seraphin B, Wilm M, Bork P, Izaurralde E (2000) REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. RNA 6:638-650
50. Vinciguerra P, Stutz F (2004) mRNA export: An assembly line from genes to nuclear pores. Curr Opin Cell Biol 16:285-292
51. Visa N, Izaurralde E, Ferreira J, Daneholt B, Mattaj IW (1996) A nuclear cap-binding complex binds Balbiani ring pre-mRNA cotranscriptionally and accompanies the ribonucleoprotein particle during nuclear export. J Cell Biol 133:5-14
52. Wutz A, Jaenisch R (2000) A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. Mol Cell 5:695-705
53. Wutz A, Rasmussen TP, Jaenisch R (2002) Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 30:167-174
54. Xing YG, Lawrence JB (1991) Preservation of specific RNA distribution within the chromatin-depleted nuclear substructure demonstrated by in situ hybridization coupled with biochemical fractionation. J Cell Biol 112:1055-1063