Dynamic chromatin localization of sirt6 shapes stress- and aging-related transcriptional networks

PLoS Genetics

Volumn 7, Issue 6, 2011, Pages

  Kawahara, Tiara L A ^a   Rapicavoli, Nicole A ^a   Wu, Angela R ^b   Qu, Kun ^a   Quake, Stephen R ^b   Chang, Howard Y ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; SIRTUIN 6; TRANSCRIPTION FACTOR RELA; TUMOR NECROSIS FACTOR ALPHA; SIRT6 PROTEIN, MOUSE; SIRTUIN;

AGING; ARTICLE; CELL AGING; CELLULAR STRESS SIGNAL; CHROMATIN; CONTROLLED STUDY; EMBRYO; GENE EXPRESSION; GENE INACTIVATION; GENE LOCATION; GENE TARGETING; GENETIC ASSOCIATION; GENETIC EPISTASIS; GENETIC TRANSCRIPTION; MOUSE; NONHUMAN; PROMOTER REGION; SENESCENCE; STRESS; WILD TYPE; ANIMAL; BIOLOGICAL MODEL; CELL LINE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; INTRACELLULAR SPACE; METABOLISM; MOUSE MUTANT; PHYSIOLOGICAL STRESS; PROTEIN TRANSPORT; REPRODUCIBILITY;

AGING; ANIMALS; CELL LINE; CHROMATIN; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; INTRACELLULAR SPACE; MICE; MICE, KNOCKOUT; MODELS, GENETIC; PROTEIN TRANSPORT; REPRODUCIBILITY OF RESULTS; SIRTUINS; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTOR RELA;

EID: 79959846078     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002153     Document Type: Article

References (44)

1. Imai S, Armstrong CM, Kaeberlein M, Guarente L, (2000) Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403: 795-800.
2. Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J, et al. (2000) The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc Natl Acad Sci U S A 97: 5807-5811.
3. Smith JS, Brachmann CB, Celic I, Kenna MA, Muhammad S, et al. (2000) A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc Natl Acad Sci U S A 97: 6658-6663.
4. Xu F, Zhang Q, Zhang K, Xie W, Grunstein M, (2007) Sir2 deacetylates histone H3 lysine 56 to regulate telomeric heterochromatin structure in yeast. Mol Cell 27: 890-900.
5. Denu JM, (2003) Linking chromatin function with metabolic networks: Sir2 family of NAD(+)-dependent deacetylases. Trends Biochem Sci 28: 41-48.
6. Frye RA, (1999) Characterization of five human cDNAs with homology to the yeast SIR2 gene: Sir2-like proteins (sirtuins) metabolize NAD and may have protein ADP-ribosyltransferase activity. Biochem Biophys Res Commun 260: 273-279.
7. Frye RA, (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 273: 793-798.
8. McCord RA, Michishita E, Hong T, Berber E, Boxer LD, et al. (2009) SIRT6 stabilizes DNA-dependent protein kinase at chromatin for DNA double-strand break repair. Aging (Albany NY) 1: 109-121.
9. Michishita E, McCord RA, Berber E, Kioi M, Padilla-Nash H, et al. (2008) SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin. Nature 452: 492-496.
10. Kawahara TL, Michishita E, Adler AS, Damian M, Berber E, et al. (2009) SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span. Cell 136: 62-74.
11. Mostoslavsky R, Chua KF, Lombard DB, Pang WW, Fischer MR, et al. (2006) Genomic instability and aging-like phenotype in the absence of mammalian SIRT6. Cell 124: 315-329.
12. Zhong LD, Urso A, Toiber D, Sebastian C, Henry RE, et al. The histone deacetylase Sirt6 regulates glucose homeostasis via Hif1alpha. Cell 140: 280-293.
13. Tennen RI, Chua KF, Chromatin regulation and genome maintenance by mammalian SIRT6. Trends Biochem Sci 36: 39-46.
14. Hayden MS, Ghosh S, (2008) Shared principles in NF-kappaB signaling. Cell 132: 344-362.
15. Hayden MS, Ghosh S, (2004) Signaling to NF-kappaB. Genes Dev 18: 2195-2224.
16. Ghosh S, May MJ, Kopp EB, (1998) NF-kappa B and Rel proteins: evolutionarily conserved mediators of immune responses. Annu Rev Immunol 16: 225-260.
17. Hoffmann A, Baltimore D, (2006) Circuitry of nuclear factor kappaB signaling. Immunol Rev 210: 171-186.
18. Foster SL, Hargreaves DC, Medzhitov R, (2007) Gene-specific control of inflammation by TLR-induced chromatin modifications. Nature 447: 972-978.
19. Adler AS, Sinha S, Kawahara TL, Zhang JY, Segal E, et al. (2007) Motif module map reveals enforcement of aging by continual NF-kappaB activity. Genes Dev 21: 3244-3257.
20. Wang Z, Zang C, Cui K, Schones DE, Barski A, et al. (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138: 1019-1031.
21. Gazin C, Wajapeyee N, Gobeil S, Virbasius CM, Green MR, (2007) An elaborate pathway required for Ras-mediated epigenetic silencing. Nature 449: 1073-1077.
22. Hoffmann A, Levchenko A, Scott ML, Baltimore D, (2002) The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science 298: 1241-1245.
23. Covert MW, Leung TH, Gaston JE, Baltimore D, (2005) Achieving stability of lipopolysaccharide-induced NF-kappaB activation. Science 309: 1854-1857.
24. Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, et al. Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 466: 267-271.
25. Schreiber J, Jenner RG, Murray HL, Gerber GK, Gifford DK, et al. (2006) Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide. Proc Natl Acad Sci U S A 103: 5899-5904.
26. Lim CA, Yao F, Wong JJ, George J, Xu H, et al. (2007) Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol Cell 27: 622-635.
27. Migliaccio E, Giorgio M, Mele S, Pelicci G, Reboldi P, et al. (1999) The p66shc adaptor protein controls oxidative stress response and life span in mammals. Nature 402: 309-313.
28. Krishnamurthy J, Torrice C, Ramsey MR, Kovalev GI, Al-Regaiey K, et al. (2004) Ink4a/Arf expression is a biomarker of aging. J Clin Invest 114: 1299-1307.
29. Janzen V, Forkert R, Fleming HE, Saito Y, Waring MT, et al. (2006) Stem-cell ageing modified by the cyclin-dependent kinase inhibitor p16INK4a. Nature 443: 421-426.
30. Brack AS, Conboy MJ, Roy S, Lee M, Kuo CJ, et al. (2007) Increased Wnt signaling during aging alters muscle stem cell fate and increases fibrosis. Science 317: 807-810.
31. Liu H, Fergusson MM, Castilho RM, Liu J, Cao L, et al. (2007) Augmented Wnt signaling in a mammalian model of accelerated aging. Science 317: 803-806.
32. De Smaele E, Zazzeroni F, Papa S, Nguyen DU, Jin R, et al. (2001) Induction of gadd45beta by NF-kappaB downregulates pro-apoptotic JNK signalling. Nature 414: 308-313.
33. Mendrysa SM, McElwee MK, Perry ME, (2001) Characterization of the 5′ and 3′ untranslated regions in murine mdm2 mRNAs. Gene 264: 139-146.
34. Mounkes LC, Kozlov S, Hernandez L, Sullivan T, Stewart CL, (2003) A progeroid syndrome in mice is caused by defects in A-type lamins. Nature 423: 298-301.
35. Wu AR, Hiatt JB, Lu R, Attema JL, Lobo NA, et al. (2009) Automated microfluidic chromatin immunoprecipitation from 2,000 cells. Lab Chip 9: 1365-1370.
36. Eriksson M, Brown WT, Gordon LB, Glynn MW, Singer J, et al. (2003) Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome. Nature 423: 293-298.
37. Southworth LK, Owen AB, Kim SK, (2009) Aging mice show a decreasing correlation of gene expression within genetic modules. PLoS Genet 5: e1000776 doi:10.1371/journal.pgen.1000776.
38. Adler AS, Kawahara TL, Segal E, Chang HY, (2008) Reversal of aging by NFkappaB blockade. Cell Cycle 7: 556-559.
39. Martin SG, Laroche T, Suka N, Grunstein M, Gasser SM, (1999) Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell 97: 621-633.
40. Oberdoerffer P, Michan S, McVay M, Mostoslavsky R, Vann J, et al. (2008) SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging. Cell 135: 907-918.
41. Perkins ND, (2007) Integrating cell-signalling pathways with NF-kappaB and IKK function. Nat Rev Mol Cell Biol 8: 49-62.
42. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, et al. Variation in transcription factor binding among humans. Science 328: 232-235.
43. Dahl JA, Collas P, (2008) A rapid micro chromatin immunoprecipitation assay (microChIP). Nat Protoc 3: 1032-1045.
44. Eisen MB, Spellman PT, Brown PO, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.