PUB-NChIP-"in vivo biotinylation" approach to study chromatin in proximity to a protein of interest

Genome Research

Volumn 23, Issue 2, 2013, Pages 331-340

  Shoaib, Muhammad ^a   Kulyyassov, Arman ^a,b   Robin, Chloé ^a   Winczura, Kinga ^a   Tarlykov, Pavel ^a,c   Despas, Emmanuelle ^a,b   Kannouche, Patricia ^a   Ramanculov, Erlan ^d   Lipinski, Marc ^a   Ogryzko, Vasily ^a  

^a UMR 8126   (France)

^b National Center of Biotechnology   (Kazakhstan)

^c L N GUMILYOV EURASIAN NATIONAL UNIVERSITY   (Kazakhstan)

^d Gustave Roussy Comprehensive Cancer Institute   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H2AZ; RAD18 PROTEIN;

ACETYLATION; ARTICLE; BIOTINYLATION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; IN VIVO STUDY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROCESSING; PROXIMITY UTILIZING BIOTINYLATION WITH NATIVE CHROMATIN IMMUNOPRECIPITATON; UBIQUITINATION;

ACETYLATION; BIOTINYLATION; CELL LINE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; HISTONES; HUMANS; NUCLEAR PROTEINS; PROTEIN PROCESSING, POST-TRANSLATIONAL;

EID: 84873387462     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.134874.111     Document Type: Article

References (44)

1. Ahmed S, Dul B, Qiu X, Walworth NC. 2007. Msc1 acts through histone H2A.Z to promote chromosome stability in Schizosaccharomyces pombe. Genetics 177: 1487-1497.
2. Bao Y. 2011. Chromatin response to DNA double-strand break damage. Epigenomics 3: 307-321.
3. Buck MJ, Lieb JD. 2004. ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83: 349-360.
4. Chadwick BP, Willard HF. 2001a. Histone H2A variants and the inactive X chromosome: Identification of a second macroH2A variant. Hum Mol Genet 10: 1101-1113.
5. Chadwick BP, Willard HF. 2001b. A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive X chromosome. J Cell Biol 152: 375-384.
6. Costanzi C, Pehrson Jr. 1998. Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals. Nature 393: 599-601.
7. Fernandez-Suarez M, Chen TS, Ting AY. 2008. Protein-protein interaction detection in vitro and in cells by proximity biotinylation. J Am Chem Soc 130: 9251-9253.
8. Garcia BA, Mollah S, Ueberheide BM, Busby SA, Muratore TL, Shabanowitz J, Hunt DF. 2007. Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat Protoc 2: 933-938.
9. Greil F, Moorman C, van Steensel B. 2006. DamID: Mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. Methods Enzymol 410: 342-359.
10. Hager GL, McNally JG, Misteli T. 2009. Transcription dynamics. Mol Cell 35: 741-753.
11. Haracska L, Johnson RE, Unk I, Phillips B, Hurwitz J, Prakash L, Prakash S. 2001a. Physical and functional interactions of human DNA polymerase h with PCNA. Mol Cell Biol 21: 7199-7206.
12. Haracska L, Johnson RE, Unk I, Phillips BB, Hurwitz J, Prakash L, Prakash S. 2001b. Targeting of human DNA polymerase i to the replication machinery via interaction with PCNA. Proc Natl Acad Sci 98: 14256-14261.
13. Huang J, Huen MS, Kim H, Leung CC, Glover JN, Yu X, Chen J. 2009. RAD18 transmits DNA damage signalling to elicit homologous recombination repair. Nat Cell Biol 11: 592-603.
14. Jenuwein T, Allis CD. 2001. Translating the histone code. Science 293: 1074-1080.
15. KalocsayM, Hiller NJ, Jentsch S. 2009. Chromosome-wide Rad51 spreading and SUMO-H2A.Z-dependent chromosome fixation in response to a persistent DNA double-strand break. Mol Cell 33: 335-343.
16. Kannouche PL, Wing J, Lehmann AR. 2004. Interaction of human DNA polymerase h with monoubiquitinated PCNA: A possible mechanism for the polymerase switch in response to DNA damage. Mol Cell 14: 491-500.
17. Kotova E, Lodhi N, Jarnik M, Pinnola AD, Ji Y, Tulin AV. 2011. Drosophila histone H2A variant (H2Av) controls poly(ADP-ribose) polymerase 1 (PARP1) activation in chromatin. Proc Natl Acad Sci 108: 6205-6210.
18. Kulyyassov A, Shoaib M, Pichugin A, Kannouche P, Ramanculov E, Lipinski M, Ogryzko V. 2011. PUB-MS: A mass-spectrometry-based method to monitor protein-protein proximity in vivo. J Proteome Res 10: 4416-4427.
19. Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR III, Abmayr SM,Washburn MP, Workman JL. 2004. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 306: 2084-2087.
20. Lambert JP, Mitchell L, Rudner A, Baetz K, Figeys D. 2009. A novel proteomics approach for the discovery of chromatin-associated protein networks. Mol Cell Proteomics 8: 870-882.
21. Madigan JP, Chotkowski HL, Glaser RL. 2002. DNA double-strand breakinduced phosphorylation of Drosophila histone variant H2Av helps prevent radiation-induced apoptosis. Nucleic Acids Res 30: 3698-3705.
22. Moldovan GL, Pfander B, Jentsch S. 2007. PCNA, the maestro of the replication fork. Cell 129: 665-679.
23. Morillo-Huesca M, Clemente-Ruiz M, Andujar E, Prado F. 2010. The SWR1 histone replacement complex causes genetic instability and genomewide transcription misregulation in the absence of H2A.Z. PLoS ONE 5: e12143. doi: 10.1371/journal.pone.0012143.
24. Negre N, Lavrov S, Hennetin J, Bellis M, Cavalli G. 2006. Mapping the distribution of chromatin proteins by ChIP on chip. Methods Enzymol 410: 316-341.
25. O'Neill LP, Turner BM. 2003. Immunoprecipitation of native chromatin: NChIP. Methods 31: 76-82.
26. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. 2002. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1: 376-386.
27. Ooi SL, Henikoff JG, Henikoff S. 2010. A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans. Nucleic Acids Res 38: e26. doi: 10.1093/nar/gkp1090.
28. Orlando V. 2000. Mapping chromosomal proteins in vivo by formaldehydecrosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25: 99-104.
29. Park PJ. 2009. ChIP-seq: Advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
30. Pesavento JJ, Kim YB, Taylor GK, Kelleher NL. 2004. Shotgun annotation of histone modifications: A new approach for streamlined characterization of proteins by top down mass spectrometry. J Am Chem Soc 126: 3386-3387.
31. Prakash S, Johnson RE, Prakash L. 2005. Eukaryotic translesion synthesis DNA polymerases: Specificity of structure and function. Annu Rev Biochem 74: 317-353.
32. Ren B, Dynlacht BD. 2004. Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol 376: 304-315.
33. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, et al. 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651-657.
34. Saade E, Mechold U, Kulyyassov A, Vertut D, Lipinski M, Ogryzko V. 2009. Analysis of interaction partners of H4 histone by a new proteomics approach. Proteomics 9: 4934-4943.
35. Shen Z, Sathyan KM, Geng Y, Zheng R, Chakraborty A, Freeman B,Wang F, Prasanth KV, Prasanth SG. 2010. A WD-repeat protein stabilizes ORC binding to chromatin. Mol Cell 40: 99-111.
36. Shevchenko A, Wilm M, Vorm O, Mann M. 1996. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal Chem 68: 850-858.
37. Svotelis A, Gevry N, Gaudreau L. 2009. Regulation of gene expression and cellular proliferation by histone H2A.Z. Biochem Cell Biol 87: 179-188.
38. van Daal A, White EM, Gorovsky MA, Elgin SC. 1988. Drosophila has a single copy of the gene encoding a highly conserved histone H2A variant of the H2A.F/Z type. Nucleic Acids Res 16: 7487-7497.
39. Van Holde KE. 1989. Chromatin. Springer-Verlag, New York.
40. van Steensel B, Henikoff S. 2000. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18: 424-428.
41. Viens A,Mechold U, Brouillard F,Gilbert C, Leclerc P,OgryzkoV. 2006. Analysis of human histone H2AZ deposition in vivo argues against its direct role in epigenetic templating mechanisms.Mol Cell Biol 26: 5325-5335.
42. Watanabe K, Iwabuchi K, Sun J, Tsuji Y, Tani T, Tokunaga K, Date T, Hashimoto M, Yamaizumi M, Tateishi S. 2009. RAD18 promotes DNA double-strand break repair during G1 phase through chromatin retention of 53BP1. Nucleic Acids Res 37: 2176-2193.
43. Weinmann AS, FarnhamPJ. 2002. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 26: 37-47.
44. Zhang L, Freitas MA, Wickham J, Parthun MR, Klisovic MI, Marcucci G, Byrd JC. 2004. Differential expression of histone post-translational modifications in acute myeloid and chronic lymphocytic leukemia determined by high-pressure liquid chromatography and mass spectrometry. J Am Soc Mass Spectrom 15: 77-86.