Revisiting the function of nuclear scaffold/matrix binding proteins in X chromosome inactivation

RNA Biology

Volumn 8, Issue 5, 2011, Pages

  Hasegawa, Yuko ^a,c   Nakagawa, Shinichi ^a,b  

^a RIKEN   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

Chromatin modifications; Epigenetics; hnRNP U SAF A; Nuclear scaffold matrix; Xist

Indexed keywords

HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; NUCLEAR SCAFFOLD MATRIX BINDING PROTEIN; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

CELL NUCLEUS; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA MODIFICATION; EPIGENETICS; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION REGULATION; GENE REPRESSION; HUMAN; NONHUMAN; PROTEIN DOMAIN; PROTEIN RNA BINDING; REVIEW; RNA PROCESSING; X CHROMOSOME INACTIVATION;

MAMMALIA;

EID: 80052822462     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.8.5.16367     Document Type: Review

References (30)

1. Brockdorff N. X-chromosome inactivation: closing in on proteins that bind Xist RNA. Trends Genet 2002; 18:352-8. (Pubitemid 34804447)
2. Heard E. Delving into the diversity of facultative heterochromatin: the epigenetics of the inactive X chromosome. Curr Opin Genet Dev 2005; 15:482-9. (Pubitemid 41262403)
3. Wutz A. Xist function: bridging chromatin and stem cells. Trends Genet 2007; 23:457-64. (Pubitemid 47259575)
4. Lee JT. The X as model for RNA's niche in epigenomic regulation. Cold Spring Harb Perspect Biol 2010; 2:3749.
5. Clemson CM, McNeil JA, Willard HF, Lawrence JB. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol 1996; 132:259-75. (Pubitemid 26052564)
6. Hasegawa Y, Brockdorff N, Kawano S, Tsutui K, Nakagawa S. The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. Dev Cell 2010; 19:469-76.
7. Deininger PL, Moran JV, Batzer MA, Kazazian HH Jr. Mobile elements and mammalian genome evolution. Curr Opin Genet Dev 2003; 13:651-8. (Pubitemid 37456885)
8. Bailey JA, Carrel L, Chakravarti A, Eichler EE. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. Proc Natl Acad Sci USA 2000; 97:6634-9. (Pubitemid 30412766)
9. Lyon MF. X-chromosome inactivation: a repeat hypothesis. Cytogenet Cell Genet 1998; 80:133-7. (Pubitemid 28330373)
10. Chow JC, Ciaudo C, Fazzari MJ, Mise N, Servant N, Glass JL, et al. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 2010; 141:956-69.
11. Berezney R. The nuclear matrix: a heuristic model for investigating genomic organization and function in the cell nucleus. J Cell Biochem 1991; 47:109-23.
12. Pederson T. Half a century of "the nuclear matrix". Mol Biol Cell 2000; 11:799-805.
13. Laemmli UK, Kas E, Poljak L, Adachi Y. Scaffold-associated regions: cis-acting determinants of chromatin structural loops and functional domains. Curr Opin Genet Dev 1992; 2:275-85.
14. Platts AE, Quayle AK, Krawetz SA. In-silico prediction and observations of nuclear matrix attachment. Cell Mol Biol Lett 2006; 11:191-213. (Pubitemid 44492477)
15. Girod PA, Nguyen DQ, Calabrese D, Puttini S, Grandjean M, Martinet D, et al. Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells. Nat Methods 2007; 4:747-53. (Pubitemid 47338170)
16. Jordan IK, Rogozin IB, Glazko GV, Koonin EV. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet 2003; 19:68-72. (Pubitemid 36120660)
17. Purbowasito W, Suda C, Yokomine T, Zubair M, Sado T, Tsutsui K, et al. Large-scale identification and mapping of nuclear matrix-attachment regions in the distal imprinted domain of mouse chromosome 7. DNA Res 2004; 11:391-407. (Pubitemid 40873614)
18. Agrelo R, Souabni A, Novatchkova M, Haslinger C, Leeb M, Komnenovic V, et al. SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells. Dev Cell 2009; 16:507-16.
19. Helbig R, Fackelmayer FO. Scaffold attachment factor A (SAF-A) is concentrated in inactive X chromosome territories through its RGG domain. Chromosoma 2003; 112:173-82. (Pubitemid 38063151)
20. Pullirsch D, Hartel R, Kishimoto H, Leeb M, Steiner G, Wutz A. The Trithorax group protein Ash2l and Saf-A are recruited to the inactive X chromosome at the onset of stable X inactivation. Development 2010; 137:935-43.
21. Fackelmayer FO, Dahm K, Renz A, Ramsperger U, Richter A. Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. Eur J Biochem 1994; 221:749-57.
22. Wutz A, Rasmussen TP, Jaenisch R. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 2002; 30:167-74.
23. Chaumeil J, Le Baccon P, Wutz A, Heard E. A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev 2006; 20:2223-37.
24. Clemson CM, Hall LL, Byron M, McNeil J, Lawrence JB. The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences. Proc Natl Acad Sci USA 2006; 103:7688-93.
25. Kim MK, Nikodem VM. hnRNP U inhibits carboxy-terminal domain phosphorylation by TFIIH and represses RNA polymerase II elongation. Mol Cell Biol 1999; 19:6833-44. (Pubitemid 29441867)
26. Martens JH, Verlaan M, Kalkhoven E, Dorsman JC, Zantema A. Scaffold/matrix attachment region elements interact with a p300-scaffold attachment factor A complex and are bound by acetylated nucleosomes. Mol Cell Biol 2002; 22:2598-606. (Pubitemid 34262982)
27. Heard E, Rougeulle C, Arnaud D, Avner P, Allis CD, Spector DL. Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell 2001; 107:727-38. (Pubitemid 34033666)
28. Mohammad F, Mondal T, Kanduri C. Epigenetics of imprinted long noncoding RNAs. Epigenetics 2009; 4:277-86.
29. Allen E, Horvath S, Tong F, Kraft P, Spiteri E, Riggs AD, et al. High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes. Proc Natl Acad Sci USA 2003; 100:9940-5. (Pubitemid 37087047)
30. Greally JM. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. Proc Natl Acad Sci USA 2002; 99:327-32. (Pubitemid 34060362)