Chromatin affinity-precipitation using a small metabolic molecule: Its application to analysis of O-acetyl-ADP-ribose

Cellular and Molecular Life Sciences

Volumn 69, Issue 4, 2012, Pages 641-650

  Tung, Shu Yun ^a   Hong, Jia Yang ^b   Walz, Thomas ^c,d   Moazed, Danesh ^d   Liou, Gunn Guang ^b,c  

^a INSTITUTE OF MOLECULAR BIOLOGY   (Taiwan)

^b NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

^c HARVARD MEDICAL SCHOOL   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Chromatin affinity precipitation (ChAP); Chromatin immunoprecipitation (ChIP); O acetyl ADP ribose (AAR, OAADPR); Silent chromatin; Sir2

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSE ACETATE; DNA FRAGMENT; SILENT INFORMATION REGULATOR PROTEIN 2;

ANALYTIC METHOD; ARTICLE; BINDING AFFINITY; BINDING ASSAY; CHROMATIN AFFINITY PRECIPITATION; CHROMATIN STRUCTURE; CONTROLLED STUDY; HETEROCHROMATIN; NONHUMAN; PROCESS DEVELOPMENT; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN LOCALIZATION;

CHROMATIN IMMUNOPRECIPITATION; CHROMOSOMES; DNA REPAIR; GENOMIC INSTABILITY; HETEROCHROMATIN; O-ACETYL-ADP-RIBOSE; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE; SIRTUIN 2;

EID: 84857054908     PISSN: 1420682X     EISSN: 14209071     Source Type: Journal    
DOI: 10.1007/s00018-011-0771-x     Document Type: Article

References (57)

1. Aparicio OM, Billington BL, Gottschling DE (1991) Modifiers of position effect are shared between telomeric and silent matingtype loci in S. cerevisiae. Cell 66:1279-1287 (Pubitemid 121001416)
2. Avalos JL, Boeke JD, Wolberger C (2004) Structural basis for the mechanism and regulation of Sir2 enzymes. Mol Cell 13:639-648 (Pubitemid 38368122)
3. Bitterman KJ, Anderson RM, Cohen HY, Latorre-Esteves M, Sinclair DA (2002) Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast Sir2 and human SIRT1. J Biol Chem 277:45099-45107 (Pubitemid 36159111)
4. Blander G, Guarente L (2004) The Sir2 family of protein deacetylases. Annu Rev Biochem 73:417-435 (Pubitemid 39050375)
5. Borra MT, O'Neill FJ, Jackson MD, Marshall B, Verdin E, Foltz KR, Denu JM (2002) Conserved enzymatic production and biological effect of O-acetyl-ADP-ribose by silent information regulator 2-like NAD?-dependent deacetylases. J Biol Chem 277:12632-12641 (Pubitemid 34952622)
6. Bryk M, Banerjee M, Murphy M, Knudsen KE, Garfinkel DJ, Curcio MJ (1997) Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev 11:255-269 (Pubitemid 27081900)
7. Carmen AA, Milne L, Grunstein M (2002) Acetylation of the yeast histone H4 N-terminus regulates its binding to heterochromatin protein SIR3. J Biol Chem 277:4778-4781 (Pubitemid 34968510)
8. Cheung P, Allis CD, Sassone-Corsi P (2000) Signaling to chromatin through histone modifications. Cell 103:263-271
9. Chou C-C, Li Y-C, Gartenberg MR (2008) Bypassing Sir2 and O-acetyl-ADP-ribose in transcriptional silencing. Mol Cell 31:650-659
10. Denu JM (2003) Linking chromatin function with metabolic networks: Sir2 family of NAD?-dependent deacetylases. Trends Biochem Sci 28:41-48 (Pubitemid 36051005)
11. Denu JM (2005) The Sir2 family of protein deacetylases. Curr Opin Chem Biol 9:431-440 (Pubitemid 41338194)
12. Gaba A, Jacobson A, Schs MS (2005) Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay. Mol Cell 20:449-460 (Pubitemid 41572301)
13. Gasser SM, Cockell MM (2001) The molecular biology of the SIR proteins. Gene 279:1-16 (Pubitemid 33145178)
14. Gottschling DE, Aparicio OM, Billington BL, Zakian VA (1990) Position effect at S. cerevisiae telomeres: reversible repression of pol II transcription. Cell 63:751-762 (Pubitemid 120035048)
15. Grubisha O, Rafty LA, Takanishi CL, Xu X, Tong L, Perraud A-L, Scharengerg AM, Denu JM (2006) Metabolite of Sir2 reaction modulates TRPM2 ion channel. J Biol Chem 281:14057-14065 (Pubitemid 43848332)
16. Grundy FJ, Henkin TM (2003) The T box and S box transcription termination control system. Fornt Biosci 8:d20-d31 (Pubitemid 39069960)
17. Guse AH (2005) Second messenger function and the structureactivity relationship of cyclic adenosine diphosphoribose (cADPR). FEBS J 272:4590-4597 (Pubitemid 41366983)
18. Hecht A, Strahl-Bolsinger S, Grunstein M (1996) Spreading of transcriptional represser SIR3 from telomeric heterochromatin. Nature 383:92-96 (Pubitemid 26296468)
19. Hecht A, Strahl-Bolsinger S, Grunstein M (1999) Mapping DNA interaction sites of chromosomal proteins crosslinking studies in yeast. Methods Mol Biol 119:469-479
20. Huang J, Moazed D (2003) Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing. Genes Dev 17:2162-2176 (Pubitemid 37052295)
21. Imai S, Armstrong CM, Kaeberlein M, Guarente L (2000) Transcriptional silencing and longevity protein Sir2 is an NADdependent histone deacetylase. Nature 403:795-800 (Pubitemid 30111843)
22. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074-1080 (Pubitemid 32758077)
23. Klar AJS, Fogel S, MacLeod K (1979) MAR1-a regulator of the HMa and HMa loci in Saccharomyces cerevisiae. Genetics 93:37-50 (Pubitemid 10154116)
24. Kustatscher G, Hothorn M, Pugieux C, Scheffzek K, Ladurner AG (2005) Splicing regulates NAD metabolite binding to histone macroH2A. Nat Struct Mol Biol 12:624-625 (Pubitemid 40980814)
25. Ladurner AG (2006) Rheostate control of gene expression by metabolites. Mol Cell 24:1-11 (Pubitemid 44466685)
26. Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J, Pillus L, Sternglanz R (2000) The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc Natl Acad Sci USA 97:5807-5811 (Pubitemid 30367480)
27. Lee S,TongL,Denu JM(2008)Quantification of endogenous sirtuin metabolite O-acetyl-ADP-ribose. Anal Biochem 15:174-179
28. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28:327-334 (Pubitemid 32702421)
29. Liou G-G, Chang HY, Lin CS, Lin-Chao S (2002) DEAD box RhlB RNAhelicase physically associateswith exoribonuclease PNPase to degrade double-stranded RNA independent of the degradosomeassembling region of RNase E. J Biol Chem 277:41157-41162 (Pubitemid 35215707)
30. Liou G-G, Tanny JC, Kruger RG, Walz T, Moazed D (2005) Assembly of the SIR complex and its regulation by O-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell 121:515-527 (Pubitemid 40720006)
31. Martino F, Kueng S, Robinson P, Tsai-Pflugfelder M, van Leeuwen F, Ziegler M, Cubizolles F, Cockell MM, Rhodes D, Gasser SM (2009) Reconstitution of yeast silent chromatin: multiple contact sites and O-AADPR binding load SIR complexes onto nucleosomes in vitro. Mol Cell 33:323-334
32. Matthews KS, Nichols JC (1998) Lactose repressor protein: functional properties and struccture. Prog Nucleic Acid Res Mol Biol 58:127-164
33. Moazed D (2001) Common themes in mechanisms of gene silencing. Mol Cell 8:489-498 (Pubitemid 32946927)
34. Moazed D, Johnson D (1996) A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell 86:667-677 (Pubitemid 26299497)
35. Moazed D, Kistler A, Axelrod A, Rine J, Johnson AD (1997) Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3. Proc Natl Acad Sci 94:2186-2191 (Pubitemid 27136849)
36. Moretti P, Freeman K, Coodly L, Shore D (1994) Evidence that a complex of SIR proteins interacts with the silencer and telomerebinding protein RAP1. Genes Dev 8:2257-2269 (Pubitemid 24314288)
37. Motta MC, Divecha N, Lemieux M, Kamel C, Chen D, Gu W, Bultsma Y, McBurney M, Guarente L (2004) Mammalian SIRT1 represses forkhead transcription factors. Cell 116:551-563 (Pubitemid 38264432)
38. North BJ, Marshall BL, Borra MT, Denu JM, Verdin E (2003) The human Sir2 ortholog, SIRT2, is an NAD ?-dependent tubulin deacetylase. Mol Cell 11:437-444 (Pubitemid 36293837)
39. Onishi M, Liou G-G, Buchberger JR, Walz T, Moazed D (2007) Role of the conserved Sir3-BAH domain in nucleosome binding and silent chromatin assembly. Mol Cell 28:1015-1028 (Pubitemid 350297032)
40. Richards EJ, Elgin SC (2002) Epigenetic codes for heterochromatin formation and silencing rounding up the usual suspects. Cell 108:489-500 (Pubitemid 34260874)
41. Rine J, Herskowitz I (1987) Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics 116:9-22
42. Rudner AD, Hall BE, Ellenberger T, Moazed D (2005) A nonhistone protein-protein interaction required for assembly of the SIR complex and silent chromatin. Mol Cell Biol 25:4514-4528 (Pubitemid 40705757)
43. Rusche LN, Kirchmaier AL, Rine J (2003) The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72:481-516 (Pubitemid 36930453)
44. Shore D (2000) The Sir2 protein family: a novel deacetylase for gene silencing and more. Proc Natl Acad Sci USA 97:14030-14032 (Pubitemid 32016521)
45. Smith JS, Boeke JD (1997) An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev 11:241-254 (Pubitemid 27081899)
46. Smith JS, Brachmann BC, Celic I, Kenna MA, Muhammad KS, Starai VJ, Avalos JL, Escalante-Semerena JC, Grubmeyer C, Wolberger C, Boeke JD (2000) A phylogenetically conserved NAD?-dependent protein deacetylase activity in the Sir2 protein family. Proc Natl Acad Sci USA 97:6658-6663 (Pubitemid 30412770)
47. Strahl-Bolsinger S, Hecht A, Luo K, Grunstein M (1997) SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev 11:83-93 (Pubitemid 27043826)
48. Tanny JC, Moazed D (2001) Coupling of histone deacetylation to NAD breakdown by the yeast silencing protein Sir2: evidence for acetyl transfer from substrate to an NAD breakdown product. Proc Natl Acad Sci 98:415-420 (Pubitemid 32105055)
49. Tanny JC, Kirkpatrick DS, Gerber SA, Gygi SP, Moazed D (2004) Budding yeast silencing complexes and regulation of Sir2 activity by protein-protein interactions. Mol Cell Biol 24:6931-6946 (Pubitemid 39014422)
50. Taunton J, Hassig CA, Schreiber ST (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272:408-411 (Pubitemid 26138177)
51. Tong L, Lee S, Denu JM (2009) Hydrolase regulates NAD? metabolites and modulates cellular REDOX. J Biol Chem 284:11256-11266
52. Turner BM (2000) Histone acetylation and an epigenetic code. BioEssays 22:836-845
53. Winkler WC, Breaker RR (2005) Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol 59:487-517 (Pubitemid 41507440)
54. Yang B, Kirchmaier L (2006) Bypassing the catalytic activity of SIR2 for SIR protein spreading in Saccharomyces cerevisiae. Mol Biol Cell 17:5287-5297 (Pubitemid 44907369)
55. Zhang J, Kaasik K, Blackburn MR, Lee CC (2006) Constant darkness is a circadian metabolic signal in mammals. Nature 439:340-343 (Pubitemid 43128859)
56. Zhao K, Chai X, Clements A, Marmorstein R (2003) Structure and autoregulation of the yeast Hst2 homolog of Sir2. Nat Struct Biol 10:864-871 (Pubitemid 37187660)
57. Zhao K, Chai X, Marmorstein R (2003) Structure of the yeast Hst2 protein deacetylase in ternary complex with 20-O-acetyl ADP ribose and histone peptide. Structure 11:1403-1411 (Pubitemid 37412422)