SAF-A forms a complex with BRG1 and both components are required for RNA polymerase II mediated transcription

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Vizlin Hodzic, Dzeneta ^a   Runnberg, Rikard ^a   Ryme, Jessica ^a   Simonsson, Stina ^b   Simonsson, Tomas ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b SAHLGRENSKA UNIVERSITY HOSPITAL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; BRG1 PROTEIN; DNA DIRECTED RNA POLYMERASE; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN U; MESSENGER RNA; RNA POLYMERASE II; DNA BINDING PROTEIN; HELICASE; NUCLEAR PROTEIN; SMARCA1 PROTEIN, HUMAN; SMARCA4 PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

ANIMAL CELL; ARTICLE; CELL DIFFERENTIATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPLEX FORMATION; CONTROLLED STUDY; EMBRYONIC STEM CELL; GENE FUNCTION; GENE INTERACTION; GENE LOCATION; GENETIC TRANSCRIPTION; IMMUNOPRECIPITATION; MOUSE; NONHUMAN; RNA INTERFERENCE; ANIMAL; BIOLOGICAL MODEL; CELL LINE; CHEMISTRY; CONFOCAL MICROSCOPY; CYTOLOGY; HUMAN; METABOLISM; METHODOLOGY; PROTEIN BINDING;

ANIMALS; CELL DIFFERENTIATION; CELL LINE; DNA HELICASES; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; EMBRYONIC STEM CELLS; HETEROGENEOUS-NUCLEAR RIBONUCLEOPROTEIN U; HUMANS; MICE; MICROSCOPY, CONFOCAL; MODELS, BIOLOGICAL; NUCLEAR PROTEINS; PROTEIN BINDING; RNA POLYMERASE II; RNA, MESSENGER; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 82755194841     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028049     Document Type: Article

References (41)

1. Orphanides G, Reinberg D, (2002) A unified theory of gene expression. Cell 108: 439-451.
2. Kingston RE, Narlikar GJ, (1999) ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes & development 13: 2339-2352.
3. Gohring F, Fackelmayer FO, (1997) The scaffold/matrix attachment region binding protein hnRNP-U (SAF-A) is directly bound to chromosomal DNA in vivo: a chemical cross-linking study. Biochemistry 36: 8276-8283.
4. Gohring F, Schwab BL, Nicotera P, Leist M, Fackelmayer FO, (1997) The novel SAR-binding domain of scaffold attachment factor A (SAF-A) is a target in apoptotic nuclear breakdown. The EMBO journal 16: 7361-7371.
5. Dreyfuss G, Matunis MJ, Pinol-Roma S, Burd CG, (1993) hnRNP proteins and the biogenesis of mRNA. Annual review of biochemistry 62: 289-321.
6. Romig H, Fackelmayer FO, Renz A, Ramsperger U, Richter A, (1992) Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. The EMBO journal 11: 3431-3440.
7. Ahmad N, Lingrel JB, (2005) Kruppel-like factor 2 transcriptional regulation involves heterogeneous nuclear ribonucleoproteins and acetyltransferases. Biochemistry 44: 6276-6285.
8. Levros LC, Do Carmo S, Edouard E, Legault P, Charfi C, et al. (2010) Characterization of nuclear factors modulating the apolipoprotein D promoter during growth arrest: implication of PARP-1, APEX-1 and ERK1/2 catalytic activities. Biochimica et biophysica acta 1803: 1062-1071.
9. Onishi Y, Hanai S, Ohno T, Hara Y, Ishida N, (2008) Rhythmic SAF-A binding underlies circadian transcription of the Bmal1 gene. Molecular and cellular biology 28: 3477-3488.
10. Vizlin-Hodzic D, Johansson H, Ryme J, Simonsson T, Simonsson S, (2011) SAF-A has a role in transcriptional regulation of Oct4 in ES cells through promoter binding. Cellular reprogramming 13: 13-27.
11. Zhao J, Ding J, Li Y, Ren K, Sha J, et al. (2009) HnRNP U mediates the long-range regulation of Shh expression during limb development. Human molecular genetics 18: 3090-3097.
12. Eggert M, Michel J, Schneider S, Bornfleth H, Baniahmad A, et al. (1997) The glucocorticoid receptor is associated with the RNA-binding nuclear matrix protein hnRNP U. The Journal of biological chemistry 272: 28471-28478.
13. Malik KF, Jaffe H, Brady J, Young WS 3rd, (1997) The class III POU factor Brn-4 interacts with other class III POU factors and the heterogeneous nuclear ribonucleoprotein U. Brain research Molecular brain research 45: 99-107.
14. Spraggon L, Dudnakova T, Slight J, Lustig-Yariv O, Cotterell J, et al. (2007) hnRNP-U directly interacts with WT1 and modulates WT1 transcriptional activation. Oncogene 26: 1484-1491.
15. Kim MK, Nikodem VM, (1999) hnRNP U inhibits carboxy-terminal domain phosphorylation by TFIIH and represses RNA polymerase II elongation. Molecular and cellular biology 19: 6833-6844.
16. Kukalev A, Nord Y, Palmberg C, Bergman T, Percipalle P, (2005) Actin and hnRNP U cooperate for productive transcription by RNA polymerase II. Nature structural & molecular biology 12: 238-244.
17. Martens JH, Verlaan M, Kalkhoven E, Dorsman JC, Zantema A, (2002) Scaffold/matrix attachment region elements interact with a p300-scaffold attachment factor A complex and are bound by acetylated nucleosomes. Molecular and cellular biology 22: 2598-2606.
18. Obrdlik A, Kukalev A, Louvet E, Farrants AK, Caputo L, et al. (2008) The histone acetyltransferase PCAF associates with actin and hnRNP U for RNA polymerase II transcription. Molecular and cellular biology 28: 6342-6357.
19. Lin RK, Hsieh YS, Lin P, Hsu HS, Chen CY, et al. (2010) The tobacco-specific carcinogen NNK induces DNA methyltransferase 1 accumulation and tumor suppressor gene hypermethylation in mice and lung cancer patients. The Journal of clinical investigation 120: 521-532.
20. Dhalluin C, Carlson JE, Zeng L, He C, Aggarwal AK, et al. (1999) Structure and ligand of a histone acetyltransferase bromodomain. Nature 399: 491-496.
21. Jacobson RH, Ladurner AG, King DS, Tjian R, (2000) Structure and function of a human TAFII250 double bromodomain module. Science 288: 1422-1425.
22. Khavari PA, Peterson CL, Tamkun JW, Mendel DB, Crabtree GR, (1993) BRG1 contains a conserved domain of the SWI2/SNF2 family necessary for normal mitotic growth and transcription. Nature 366: 170-174.
23. Shen W, Xu C, Huang W, Zhang J, Carlson JE, et al. (2007) Solution structure of human Brg1 bromodomain and its specific binding to acetylated histone tails. Biochemistry 46: 2100-2110.
24. Subtil-Rodriguez A, Reyes JC, (2010) BRG1 helps RNA polymerase II to overcome a nucleosomal barrier during elongation, in vivo. EMBO reports 11: 751-757.
25. Ho L, Ronan JL, Wu J, Staahl BT, Chen L, et al. (2009) An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proceedings of the National Academy of Sciences of the United States of America 106: 5181-5186.
26. Reyes JC, Muchardt C, Yaniv M, (1997) Components of the human SWI/SNF complex are enriched in active chromatin and are associated with the nuclear matrix. The Journal of cell biology 137: 263-274.
27. Kim SI, Bresnick EH, Bultman SJ, (2009) BRG1 directly regulates nucleosome structure and chromatin looping of the alpha globin locus to activate transcription. Nucleic acids research 37: 6019-6027.
28. Neish AS, Anderson SF, Schlegel BP, Wei W, Parvin JD, (1998) Factors associated with the mammalian RNA polymerase II holoenzyme. Nucleic acids research 26: 847-853.
29. Kidder BL, Palmer S, Knott JG, (2009) SWI/SNF-Brg1 regulates self-renewal and occupies core pluripotency-related genes in embryonic stem cells. Stem cells 27: 317-328.
30. Bultman S, Gebuhr T, Yee D, La Mantia C, Nicholson J, et al. (2000) A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. Molecular cell 6: 1287-1295.
31. Muchardt C, Bourachot B, Reyes JC, Yaniv M, (1998) ras transformation is associated with decreased expression of the brm/SNF2alpha ATPase from the mammalian SWI-SNF complex. The EMBO journal 17: 223-231.
32. Roshon MJ, Ruley HE, (2005) Hypomorphic mutation in hnRNP U results in post-implantation lethality. Transgenic research 14: 179-192.
33. Soderberg O, Gullberg M, Jarvius M, Ridderstrale K, Leuchowius KJ, et al. (2006) Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nature methods 3: 995-1000.
34. Batsche E, Yaniv M, Muchardt C, (2006) The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nature structural & molecular biology 13: 22-29.
35. Smith AG, Heath JK, Donaldson DD, Wong GG, Moreau J, et al. (1988) Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides. Nature 336: 688-690.
36. Williams RL, Hilton DJ, Pease S, Willson TA, Stewart CL, et al. (1988) Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells. Nature 336: 684-687.
37. Asp P, Wihlborg M, Karlen M, Farrants AK, (2002) Expression of BRG1, a human SWI/SNF component, affects the organisation of actin filaments through the RhoA signalling pathway. Journal of cell science 115: 2735-2746.
38. Kawano S, Miyaji M, Ichiyasu S, Tsutsui KM, Tsutsui K, (2010) Regulation of DNA Topoisomerase IIbeta through RNA-dependent association with heterogeneous nuclear ribonucleoprotein U (hnRNP U). The Journal of biological chemistry 285: 26451-26460.
39. Liu K, Luo Y, Lin FT, Lin WC, (2004) TopBP1 recruits Brg1/Brm to repress E2F1-induced apoptosis, a novel pRb-independent and E2F1-specific control for cell survival. Genes & development 18: 673-686.
40. Luo L, Gassman KL, Petell LM, Wilson CL, Bewersdorf J, et al. (2009) The nuclear periphery of embryonic stem cells is a transcriptionally permissive and repressive compartment. Journal of cell science 122: 3729-3737.
41. Nagy A, Rossant J, Nagy R, Abramow-Newerly W, Roder JC, (1993) Derivation of completely cell culture-derived mice from early-passage embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America 90: 8424-8428.