Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 14, 2011, Pages 5572-5577

  Strübbe, Gero ^a   Popp, Christian ^b   Schmidt, Alexander ^a,f   Pauli, Andrea ^c,g   Ringrose, Leonie ^d   Beisel, Christian ^a   Paro, Renato ^a,e  

^a ETH ZURICH   (Switzerland)

^b BABRAHAM INSTITUTE   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

^e UNIVERSITY OF BASEL   (Switzerland)

^f UNIVERSITY OF BASEL   (Switzerland)

^g HARVARD UNIVERSITY   (United States)

Author keywords

Biotagging; BirA; Pairing sensitive silencing; Proteomics

Indexed keywords

COHESIN; POLYCOMB GROUP PROTEIN; REGULATOR PROTEIN; TRITHORAX PROTEIN; UNCLASSIFIED DRUG;

BIOTINYLATION; CONFERENCE PAPER; CONTROLLED STUDY; DROSOPHILA; EMBRYO; GENE SILENCING; MASS SPECTROMETRY; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN ISOLATION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PURIFICATION; REPORTER GENE; STOICHIOMETRY; TRANSGENE;

EID: 79955016832     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1007916108     Document Type: Article

References (39)

1. Simon JA, Kingston RE (2009) Mechanisms of polycomb gene silencing: Knowns and unknowns. Nat Rev Mol Cell Biol 10:697-708.
2. Surface LE, Thornton SR, Boyer LA (2010) Polycomb group proteins set the stage for early lineage commitment. Cell Stem Cell 7:288-298.
3. Ringrose L, Paro R (2007) Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 134:223-232.
4. Muller J, Verrijzer P (2009) Biochemical mechanisms of gene regulation by polycomb group protein complexes. Curr Opin Genet Dev 19:150-158.
5. de Boer E, et al. (2003) Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci USA 100:7480-7485. (Pubitemid 36759995)
6. Rodriguez P, et al. (2006) Isolation of transcription factor complexes by in vivo biotinylation tagging and direct binding to streptavidin beads (Translated from eng). Methods Mol Biol 338:305-323 (in eng).
7. Tagwerker C, et al. (2006) A tandem affinity tag for two-step purification under fully denaturing conditions: Application in ubiquitin profiling and protein complex identification combined with in vivocross-linking. Mol Cell Proteomics 5:737-748.
8. Furuyama T, Henikoff S (2006) Biotin-tag affinity purification of a centromeric nucleosome assembly complex. Cell Cycle 5:1269-1274. (Pubitemid 43894278)
9. Wang J, et al. (2006) A protein interaction network for pluripotency of embryonic stem cells. Nature 444:364-368. (Pubitemid 44764111)
10. Lee TI, et al. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125:301-313. (Pubitemid 44313811)
11. Boyer LA, et al. (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441:349-353. (Pubitemid 44050199)
12. Kim J, Chu J, Shen X, Wang J, Orkin SH (2008) An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132:1049-1061. (Pubitemid 351381745)
13. Mito Y, Henikoff JG, Henikoff S (2005) Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet 37:1090-1097. (Pubitemid 41486661)
14. Duffy JB (2002) GAL4 system in Drosophila: A fly geneticist's Swiss army knife. Genesis 34:1-15.
15. Paro R, Hogness DS (1991) The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. Proc Natl Acad Sci USA 88:263-267. (Pubitemid 21914467)
16. Shao Z, et al. (1999) Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell 98:37-46. (Pubitemid 29331194)
17. Saurin AJ, Shao Z, Erdjument Bromage H, Tempst P, Kingston RE (2001) A Drosophila Polycomb group complex includes Zeste and dTAFII proteins. Nature 412:655-660.
18. Klymenko T, et al. (2006) A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities. Genes Dev 20:1110-1122.
19. Tuckfield A, et al. (2002) Binding of the RING polycomb proteins to specific target genes in complex with the grainyhead-like family of developmental transcription factors. Mol Cell Biol 22:1936-1946. (Pubitemid 34175008)
20. Chang YL, King B, Lin SC, Kennison JA, Huang DH (2007) A double-bromodomain protein, FSH-S, activates the homeotic gene ultrabithorax through a critical promoter- proximal region. Mol Cell Biol 27:5486-5498. (Pubitemid 47124401)
21. Yang XJ, Ullah M (2007) MOZ and MORF, two large MYSTic HATs in normal and cancer stem cells. Oncogene 26:5408-5419. (Pubitemid 47255923)
22. Laue K, et al. (2008) The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity. Development 135:1935-1946. (Pubitemid 351943358)
23. Ullah M, et al. (2008) Molecular architecture of quartet MOZ/MORF histone acetyltransferase complexes. Mol Cell Biol 28:6828-6843.
24. Pintard L, Willems A, Peter M (2004) Cullin-based ubiquitin ligases: Cul3-BTB complexes join the family. EMBO J 23:1681-1687. (Pubitemid 38649631)
25. Boulton SJ, Brook A, Staehling Hampton K, Heitzler P, Dyson N (2000) A role for Ebi in neuronal cell cycle control. EMBO J 19:5376-5386.
26. Nasmyth K, Haering CH (2009) Cohesin: Its roles and mechanisms. Annu Rev Genet 43:525-58.
27. Pauli A, et al. (2008) Cell-type-specific TEV protease cleavage reveals cohesin functions in Drosophila neurons. Dev Cell 14:239-251. (Pubitemid 351189182)
28. Dorsett D (2009) Cohesin, gene expression and development: Lessons from Drosophila. Chromosome Res 17:185-200.
29. Hallson G, et al. (2008) The Drosophila cohesin subunit Rad21 is a trithorax group (trxG) protein. Proc Natl Acad Sci USA 105:12405-12410.
30. Lagarou A, et al. (2008) dKDM2 couples histone H2A ubiquitylation to histone H3 demethylation during Polycomb group silencing. Genes Dev 22:2799-2810.
31. Kassis JA (2002) Pairing-sensitive silencing, polycomb group response elements, and transposon homing in Drosophila. Adv Genet 46:421-438.
32. Lewis JP, Tanke HJ, Raap AK, Beverstock GC, Kluin-Nelemans HC (1993) Somatic pairing of centromeres and short arms of chromosome 15 in the hematopoietic and lymphoid system. Hum Genet 92:577-582. (Pubitemid 23356816)
33. Revenkova E, Jessberger R (2005) Keeping sister chromatids together: cohesins in meiosis. Reproduction 130:783-790. (Pubitemid 41830088)
34. Schmitt S, Prestel M, Paro R (2005) Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev 19:697-708. (Pubitemid 40395081)
35. Rudenko A, Bennett D, Alphey L (2003) Trithorax interactswith type 1 serine/threonine protein phosphatase in Drosophila. EMBO Rep 4:59-63. (Pubitemid 36305379)
36. Yokoyama A, et al. (2004) Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Mol Cell Biol 24:5639-5649. (Pubitemid 38787950)
37. Scott EK, Lee T, Luo L (2001) enok encodes a Drosophila putative histone acetyltransferase required for mushroom body neuroblast proliferation. Curr Biol 11:99-104. (Pubitemid 32116841)
38. O'Dor E, Beck SA, Brock HW (2006) Polycomb group mutants exhibit mitotic defects in syncytial cell cycles of Drosophila embryos. Dev Biol 290:312-322. (Pubitemid 43163494)
39. Kamakaka RT, Tyree CM, Kadonaga JT (1991) Accurate and efficient RNA polymerase II transcription with a soluble nuclear fraction derived from Drosophila embryos. Proc Natl Acad Sci USA 88:1024-1028. (Pubitemid 21916157)