Global and specific responses of the histone acetylome to systematic perturbation

Molecular Cell

Volumn 57, Issue 3, 2015, Pages 559-571

  Feller, Christian ^a,b   Forné, Ignasi ^a   Imhof, Axel ^a   Becker, Peter B ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ACYLTRANSFERASE; HISTONE ACETYLTRANSFERASE; HISTONE H3; HISTONE H4; LYSINE; DROSOPHILA PROTEIN; HISTONE; HISTONE DEACETYLASE;

ARTICLE; CHROMATIN; DROSOPHILA; ENZYME SPECIFICITY; GENE EXPRESSION REGULATION; HISTONE ACETYLATION; HISTONE METHYLATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; X CHROMOSOME; ACETYLATION; ANIMAL; CELL LINE; DROSOPHILA MELANOGASTER; ENZYMOLOGY; HUMAN; METABOLISM; METHYLATION; PROTEOMICS;

EUKARYOTA;

ACETYLATION; ANIMALS; CELL LINE; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; HISTONE ACETYLTRANSFERASES; HISTONE DEACETYLASES; HISTONES; HUMANS; LYSINE; MASS SPECTROMETRY; METHYLATION; PROTEOMICS;

EID: 84924875114     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2014.12.008     Document Type: Article

References (41)

1. Allis C.D., Berger S.L., Cote J., Dent S., Jenuwien T., Kouzarides T., Pillus L., Reinberg D., Shi Y., Shiekhattar R., et al. New nomenclature for chromatin-modifying enzymes. Cell 2007, 131:633-636.
2. Bodenmiller B., Wanka S., Kraft C., Urban J., Campbell D., Pedrioli P.G., Gerrits B., Picotti P., Lam H., Vitek O., et al. Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci. Signal. 2010, 3:rs4.
3. Cai Y., Jin J., Swanson S.K., Cole M.D., Choi S.H., Florens L., Washburn M.P., Conaway J.W., Conaway R.C. Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. J.Biol. Chem. 2010, 285:4268-4272.
4. Chelmicki T., Dundar F., Turley M.J., Khanam T., Aktas T., Ramirez F., Gendrel A.V., Wright P.R., Videm P., Backofen R., et al. MOF-associated complexes ensure stem cell identity and Xist repression. eLife 2014, 3:e02024.
5. Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 2009, 325:834-840.
6. Clark D.J., Kimura T. Electrostatic mechanism of chromatin folding. J.Mol. Biol. 1990, 211:883-896.
7. Conrad T., Cavalli F.M., Holz H., Hallacli E., Kind J., Ilik I., Vaquerizas J.M., Luscombe N.M., Akhtar A. The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex. Dev. Cell 2012, 22:610-624.
8. Dawson M.A., Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell 2012, 150:12-27.
9. Feller C., Prestel M., Hartmann H., Straub T., Söding J., Becker P.B. The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset. Nucleic Acids Res. 2012, 40:1509-1522.
10. Filippakopoulos P., Picaud S., Mangos M., Keates T., Lambert J.P., Barsyte-Lovejoy D., Felletar I., Volkmer R., Müller S., Pawson T., et al. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 2012, 149:214-231.
11. Fischle W., Wang Y., Allis C.D. Histone and chromatin cross-talk. Curr. Opin. Cell Biol. 2003, 15:172-183.
12. Fuchs S.M., Krajewski K., Baker R.W., Miller V.L., Strahl B.D. Influence of combinatorial histone modifications on antibody and effector protein recognition. Curr. Biol. 2011, 21:53-58.
13. Garcia B.A., Mollah S., Ueberheide B.M., Busby S.A., Muratore T.L., Shabanowitz J., Hunt D.F. Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protoc. 2007, 2:933-938.
14. Gräff J., Tsai L.H. Histone acetylation: molecular mnemonics on the chromatin. Nat. Rev. Neurosci. 2013, 14:97-111.
15. Gu W., Szauter P., Lucchesi J.C. Targeting of MOF, a putative histone acetyl transferase, to the X chromosome of Drosophila melanogaster. Dev. Genet. 1998, 22:56-64.
16. Jin Q., Yu L.R., Wang L., Zhang Z., Kasper L.H., Lee J.E., Wang C., Brindle P.K., Dent S.Y., Ge K. Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO J. 2011, 30:249-262.
17. Jung H.R., Sidoli S., Haldbo S., Sprenger R.R., Schwämmle V., Pasini D., Helin K., Jensen O.N. Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS. Anal. Chem. 2013, 85:8232-8239.
18. 2-M DNA damage checkpoint. Sci. Signal. 2011, 4:rs1.
19. Kouzarides T. Chromatin modifications and their function. Cell 2007, 128:693-705.
20. Kueh A.J., Dixon M.P., Voss A.K., Thomas T. HBO1 is required for H3K14 acetylation and normal transcriptional activity during embryonic development. Mol. Cell. Biol. 2011, 31:845-860.
21. Lam K.C., Mühlpfordt F., Vaquerizas J.M., Raja S.J., Holz H., Luscombe N.M., Manke T., Akhtar A. The NSL complex regulates housekeeping genes in Drosophila. PLoS Genet. 2012, 8:e1002736.
22. Lee K.K., Workman J.L. Histone acetyltransferase complexes: one size doesn't fit all. Nat. Rev. Mol. Cell Biol. 2007, 8:284-295.
23. Lin S., Wein S., Gonzales-Cope M., Otte G.L., Yuan Z.F., Afjehi-Sadat L., Maile T., Berger S.L., Rush J., Lill J.R., et al. Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry. Mol. Cell. Proteomics 2014, 13:2450-2466.
24. Marx H., Lemeer S., Schliep J.E., Matheron L., Mohammed S., Cox J., Mann M., Heck A.J., Kuster B. A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat. Biotechnol. 2013, 31:557-564.
25. Parthun M.R. Histone acetyltransferase 1: more than just an enzyme?. Biochim. Biophys. Acta 2012, 1819:256-263.
26. Pesavento J.J., Bullock C.R., LeDuc R.D., Mizzen C.A., Kelleher N.L. Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry. J.Biol. Chem. 2008, 283:14927-14937.
27. Plazas-Mayorca M.D., Bloom J.S., Zeissler U., Leroy G., Young N.L., DiMaggio P.A., Krugylak L., Schneider R., Garcia B.A. Quantitative proteomics reveals direct and indirect alterations in the histone code following methyltransferase knockdown. Mol. Biosyst. 2010, 6:1719-1729.
28. Prestel M., Feller C., Becker P.B. Dosage compensation and the global re-balancing of aneuploid genomes. Genome Biol. 2010, 11:216.
29. Prestel M., Feller C., Straub T., Mitlöhner H., Becker P.B. The activation potential of MOF is constrained for dosage compensation. Mol. Cell 2010, 38:815-826.
30. Rothbart S.B., Lin S., Britton L.M., Krajewski K., Keogh M.C., Garcia B.A., Strahl B.D. Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies. Sci. Rep. 2012, 2:489.
31. Ruthenburg A.J., Li H., Patel D.J., Allis C.D. Multivalent engagement of chromatin modifications by linked binding modules. Nat. Rev. Mol. Cell Biol. 2007, 8:983-994.
32. Schotta G., Sengupta R., Kubicek S., Malin S., Kauer M., Callén E., Celeste A., Pagani M., Opravil S., De La Rosa-Velazquez I.A., et al. A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse. Genes Dev. 2008, 22:2048-2061.
33. Sinha I., Buchanan L., Rönnerblad M., Bonilla C., Durand-Dubief M., Shevchenko A., Grunstein M., Stewart A.F., Ekwall K. Genome-wide mapping of histone modifications and mass spectrometry reveal H4 acetylation bias and H3K36 methylation at gene promoters in fission yeast. Epigenomics 2010, 2:377-393.
34. Smith C.M., Gafken P.R., Zhang Z., Gottschling D.E., Smith J.B., Smith D.L. Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4. Anal. Biochem. 2003, 316:23-33.
35. Smith E.R., Cayrou C., Huang R., Lane W.S., CÔté J., Lucchesi J.C. A human protein complex homologous to the Drosophila MSL complex is responsible for the majority of histone H4 acetylation at lysine 16. Mol. Cell. Biol. 2005, 25:9175-9188.
36. Sterner D.E., Berger S.L. Acetylation of histones and transcription-related factors. Microbiol. Mol. Biol. Rev. 2000, 64:435-459.
37. Tan M., Luo H., Lee S., Jin F., Yang J.S., Montellier E., Buchou T., Cheng Z., Rousseaux S., Rajagopal N., et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 2011, 146:1016-1028.
38. Vizcaíno J.A., Deutsch E.W., Wang R., Csordas A., Reisinger F., Ríos D., Dianes J.A., Sun Z., Farrah T., Bandeira N., et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol. 2014, 32:223-226.
39. Voss A.K., Thomas T. MYST family histone acetyltransferases take center stage in stem cells and development. BioEssays 2009, 31:1050-1061.
40. Young N.L., DiMaggio P.A., Plazas-Mayorca M.D., Baliban R.C., Floudas C.A., Garcia B.A. High throughput characterization of combinatorial histone codes. Mol. Cell. Proteomics 2009, 8:2266-2284.
41. Zheng Y., Thomas P.M., Kelleher N.L. Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites. Nat. Comm. 2013, 4:2203.