Incorporating DNA shearing in standard affinity purification allows simultaneous identification of both soluble and chromatin-bound interaction partners

Journal of Proteomics

Volumn 100, Issue , 2014, Pages 55-59

  Lambert, Jean Philippe ^a   Tucholska, Monika ^a   Pawson, Tony ^a,b   Gingras, Anne Claude ^a,b  

^a MOUNT SINAI HOSPITAL   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Affinity purification coupled to mass spectrometry; Chromatin; Protein protein interactions; Systems biology

Indexed keywords

DNA; HISTONE; CHROMATIN;

AFFINITY PURIFICATION COUPLED MASS SPECTROMETRY; ARTICLE; CHROMATIN; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; SYSTEMS BIOLOGY; ULTRASOUND; AFFINITY CHROMATOGRAPHY; CHEMISTRY; DNA FRAGMENTATION; ISOLATION AND PURIFICATION; METABOLISM; PROCEDURES; SOLUBILITY;

CHROMATIN; CHROMATOGRAPHY, AFFINITY; DNA; DNA FRAGMENTATION; HISTONES; MASS SPECTROMETRY; SOLUBILITY;

EID: 84897032710     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.12.022     Document Type: Article

References (20)

1. Bannister A.J., Kouzarides T. Regulation of chromatin by histone modifications. Cell Res 2011, 21:381-395.
2. Lambert J.P., Pawson T., Gingras A.C. Mapping physical interactions within chromatin by proteomic approaches. Proteomics 2012, 12:1609-1622.
3. Sidoli S., Cheng L., Jensen O.N. Proteomics in chromatin biology and epigenetics: elucidation of post-translational modifications of histone proteins by mass spectrometry. J Proteomics 2012, 75:3419-3433.
4. Mak A.B., Ni Z., Hewel J.A., Chen G.I., Zhong G., Karamboulas K., et al. A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. Mol Cell Proteomics 2010, 9:811-823.
5. Foltz D.R., Jansen L.E., Black B.E., Bailey A.O., Yates J.R., Cleveland D.W. The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol 2006, 8:458-469.
6. Lambert J.P., Fillingham J., Siahbazi M., Greenblatt J., Baetz K., Figeys D. Defining the budding yeast chromatin-associated interactome. Mol Syst Biol 2010, 6:448.
7. Glatter T., Wepf A., Aebersold R., Gstaiger M. An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol 2009, 5:237.
8. Dunham W.H., Mullin M., Gingras A.C. Affinity-purification coupled to mass spectrometry: basic principles and strategies. Proteomics 2012, 12:1576-1590.
9. Liu G., Zhang J., Larsen B., Stark C., Breitkreutz A., Lin Z.Y., et al. ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol 2010, 28:1015-1017.
10. Eng J.K., Jahan T.A., Hoopmann M.R. Comet: an open-source MS/MS sequence database search tool. Proteomics 2013, 13:22-24.
11. Shteynberg D., Deutsch E.W., Lam H., Eng J.K., Sun Z., Tasman N., et al. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics 2011, 10:M111. [007690].
12. Choi H., Larsen B., Lin Z.Y., Breitkreutz A., Mellacheruvu D., Fermin D., et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 2011, 8:70-73.
13. Campos E.I., Fillingham J., Li G., Zheng H., Voigt P., Kuo W.H., et al. The program for processing newly synthesized histones H3.1 and H4. Nat Struct Mol Biol 2010, 17:1343-1351.
14. Lambert J.P., Mitchell L., Rudner A., Baetz K., Figeys D. A novel proteomics approach for the discovery of chromatin-associated protein networks. Mol Cell Proteomics 2009, 8:870-882.
15. Filippakopoulos P., Picaud S., Mangos M., Keates T., Lambert J.P., Barsyte-Lovejoy D., et al. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 2012, 149:214-231.
16. Drane P., Ouararhni K., Depaux A., Shuaib M., Hamiche A. The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. Genes Dev 2010, 24:1253-1265.
17. Zhang Y., LeRoy G., Seelig H.P., Lane W.S., Reinberg D. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell 1998, 95:279-289.
18. Foltz D.R., Jansen L.E., Bailey A.O., Yates J.R., Bassett E.A., Wood S., et al. Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell 2009, 137:472-484.
19. Mellacheruvu D., Wright Z., Couzens A.L., Lambert J.-P., St-Denis N., Li T., et al. The CRAPome: a contaminant repository for afffinity purification mass spectrometry data. Nat Methods 2013, 10:730-736.
20. Schwartzentruber J., Korshunov A., Liu X.Y., Jones D.T., Pfaff E., Jacob K., et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 2012, 482:226-231.