96
Views
34
CrossRef citations to date
0
Altmetric
Article

Histone Methylation Has Dynamics Distinct from Those of Histone Acetylation in Cell Cycle Reentry from Quiescence

, , , , &
Pages 3968-3980 | Received 06 Jun 2014, Accepted 14 Aug 2014, Published online: 20 Mar 2023

REFERENCES

  • Sang L, Coller HA, Roberts JM. 2008. Control of the reversibility of cellular quiescence by the transcriptional repressor HES1. Science 321:1095–1100. http://dx.doi.org/10.1126/science.1155998.
  • Pardee AB. 1974. A restriction point for control of normal animal cell proliferation. Proc. Natl. Acad. Sci. U. S. A. 71:1286–1290. http://dx.doi.org/10.1073/pnas.71.4.1286.
  • Gray JV, Petsko GA, Johnston GC, Ringe D, Singer RA, Werner-Washburne M. 2004. “Sleeping Beauty”: Quiescence in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 68:187–206. http://dx.doi.org/10.1128/MMBR.68.2.187-206.2004.
  • Martinez MJ, Roy S, Archuletta AB, Wentzell PD, Anna-arriola SS, Rodriguez AL, Aragon AD, Quin GA, Allen C, Werner-washburne M. 2004. Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes. Mol. Biol. Cell 15:5295–5305. http://dx.doi.org/10.1091/mbc.E03-11-0856.
  • Slattery MG, Heideman W. 2007. Coordinated regulation of growth genes in Saccharomyces cerevisiae. Cell Cycle 1210–1219. http://dx.doi.org/10.4161/cc.6.10.4257.
  • Radonjic M, Andrau J-C, Lijnzaad P, Kemmeren P, Kockelkorn TTJP, van Leenen D, van Berkum NL, Holstege FCP. 2005. Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol. Cell 18:171–183. http://dx.doi.org/10.1016/j.molcel.2005.03.010.
  • Kaelin WG, McKnight SL. 2013. Influence of metabolism on epigenetics and disease. Cell 153:56–69. http://dx.doi.org/10.1016/j.cell.2013.03.004.
  • Lu C, Thompson CB. 2012. Metabolic regulation of epigenetics. Cell Metab. 16:9–17. http://dx.doi.org/10.1016/j.cmet.2012.06.001.
  • Laporte D, Lebaudy A, Sahin A, Pinson B, Ceschin J, Daignan-Fornier B, Sagot I. 2011. Metabolic status rather than cell cycle signals control quiescence entry and exit. J. Cell Biol. 192:949–957. http://dx.doi.org/10.1083/jcb.201009028.
  • Cai L, Sutter BM, Li B, Tu BP. 2011. Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol. Cell 42:426–437. http://dx.doi.org/10.1016/j.molcel.2011.05.004.
  • Friis RMN, Wu BP, Reinke SN, Hockman DJ, Sykes BD, Schultz MC. 2009. A glycolytic burst drives glucose induction of global histone acetylation by picNuA4 and SAGA. Nucleic Acids Res. 37:3969–3980. http://dx.doi.org/10.1093/nar/gkp270.
  • Fox CJ, Hammerman PS, Thompson CB. 2005. Fuel feeds function: energy metabolism and the T-cell response. Nat. Rev. Immunol. 5:844–852. http://dx.doi.org/10.1038/nri1710.
  • Taplick J, Kurtev V, Lagger G, Seiser C. 1998. Histone H4 acetylation during interleukin-2 stimulation of mouse T cells. FEBS Lett. 436:349–352. http://dx.doi.org/10.1016/S0014-5793(98)01164-8.
  • Wellen KE, Hatzivassiliou G, Sachdeva UM, Bui TV, Cross JR, Thompson CB. 2009. ATP-citrate lyase links cellular metabolism to histone acetylation. Science 324:1076–1080. http://dx.doi.org/10.1126/science.1164097.
  • Katada S, Imhof A, Sassone-Corsi P. 2012. Connecting threads: epigenetics and metabolism. Cell 148:24–28. http://dx.doi.org/10.1016/j.cell.2012.01.001.
  • Evertts AG, Zee BM, Dimaggio PA, Gonzales-Cope M, Coller HA, Garcia BA. 2013. Quantitative dynamics of the link between cellular metabolism and histone acetylation. J. Biol. Chem. 288:12142–12151. http://dx.doi.org/10.1074/jbc.M112.428318.
  • Klose RJ, Zhang Y. 2007. Regulation of histone methylation by demethylimination and demethylation. Nat. Rev. Mol. Cell Biol. 8:307–318. http://dx.doi.org/10.1038/nrm2143.
  • Teperino R, Schoonjans K, Auwerx J. 2010. Histone methyl transferases and demethylases; can they link metabolism and transcription? Cell Metab. 12:321–327. http://dx.doi.org/10.1016/j.cmet.2010.09.004.
  • Katoh Y, Ikura T, Hoshikawa Y, Tashiro S, Ito T, Ohta M, Kera Y, Noda T, Igarashi K. 2011. Methionine adenosyltransferase II serves as a transcriptional corepressor of Maf oncoprotein. Mol. Cell 41:554–566. http://dx.doi.org/10.1016/j.molcel.2011.02.018.
  • Shyh-Chang N, Locasale JW, Lyssiotis CA, Zheng Y, Teo RY, Ratanasirintrawoot S, Zhang J, Onder T, Unternaehrer JJ, Zhu H, Asara JM, Daley GQ, Cantley LC. 2013. Influence of threonine metabolism on S-adenosylmethionine and histone methylation. Science 339:222–226. http://dx.doi.org/10.1126/science.1226603.
  • Zee BM, Levin RS, Xu B, LeRoy G, Wingreen NS, Garcia Ba. 2010. In vivo residue-specific histone methylation dynamics. J. Biol. Chem. 285:3341–3350. http://dx.doi.org/10.1074/jbc.M109.063784.
  • Fabrizio P, Longo VD. 2003. The chronological life span of Saccharomyces cerevisiae. Aging Cell 2:73–81. http://dx.doi.org/10.1046/j.1474-9728.2003.00033.x.
  • Kizer KO, Xiao T, Strahl BD. 2006. Accelerated nuclei preparation and methods for analysis of histone modifications in yeast. Methods 40:296–302. http://dx.doi.org/10.1016/j.ymeth.2006.06.022.
  • Recht J, Tsubota T, Tanny JC, Diaz RL, Berger JM, Zhang X, Garcia BA, Shabanowitz J, Burlingame A, Hunt LDF, Kaufman PD, Allis CD. 2006. Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis. Proc. Natl. Acad. Sci. U. S. A. 103:6988–6993. http://dx.doi.org/10.1073/pnas.0601676103.
  • Lin S, Garcia Ba. 2012. Examining histone posttranslational modification patterns by high-resolution mass spectrometry. Methods Enzymol. 512:3–28. http://dx.doi.org/10.1016/B978-0-12-391940-3.00001-9.
  • Bajad SU, Lu W, Kimball EH, Yuan J, Peterson C, Rabinowitz JD. 2006. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J. Chromatogr. A 1125:76–88. http://dx.doi.org/10.1016/j.chroma.2006.05.019.
  • Zee BM, Britton L-MP, Wolle D, Haberman DM, Garcia BA. 2012. Origins and formation of histone methylation across the human cell cycle. Mol. Cell. Biol. 32:2503–2514. http://dx.doi.org/10.1128/MCB.06673-11.
  • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111. http://dx.doi.org/10.1093/bioinformatics/btp120.
  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28:511–515. http://dx.doi.org/10.1038/nbt.1621.
  • Wyce A, Xiao T, Whelan KA, Kosman C, Walter W, Eick D, Hughes TR, Krogan NJ, Strahl BD, Berger SL. 2007. H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex. Mol. Cell 27:275–288. http://dx.doi.org/10.1016/j.molcel.2007.01.035.
  • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25. http://dx.doi.org/10.1186/gb-2009-10-3-r25.
  • Katada S, Imhof A, Sassone-Corsi P. 2012. Connecting threads: epigenetics and metabolism. Cell 148:24–28. http://dx.doi.org/10.1016/j.cell.2012.01.001.
  • Ong S-E. 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. http://dx.doi.org/10.1074/mcp.M200025-MCP200.
  • Wang Y, Pierce M, Schneper L, Güldal CG, Zhang X, Tavazoie S, Broach JR. 2004. Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. PLoS Biol. 2:E128. http://dx.doi.org/10.1371/journal.pbio.0020128.
  • Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11:4241–4257. http://dx.doi.org/10.1091/mbc.11.12.4241.
  • Slattery M, Heideman W. 2007. Coordinated regulation of growth genes in Saccharomyces cerevisiae. Cell Cycle 6:1210–1219. http://dx.doi.org/10.4161/cc.6.10.4257.
  • Gut P, Verdin E. 2013. The nexus of chromatin regulation and intermediary metabolism. Nature 502:489–498. http://dx.doi.org/10.1038/nature12752.
  • Byvoet P, Shepherd GR, Hardin JM, Noland BJ. 1972. The distribution and turnover of labeled methyl groups in histone fractions of cultured mammalian cells. Arch. Biochem. Biophys. 148:558–567. http://dx.doi.org/10.1016/0003-9861(72)90174-9.
  • Byvoet P. 1972. In vivo turnover and distribution of radio-N-methyl in arginine-rich histones from rat tissues. Arch. Biochem. Biophys. 152:887–888. http://dx.doi.org/10.1016/0003-9861(72)90286-X.
  • Anand R, Marmorstein R. 2007. Structure and mechanism of lysine-specific demethylase enzymes. J. Biol. Chem. 282:35425–35429. http://dx.doi.org/10.1074/jbc.R700027200.
  • Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y. 2006. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439:811–816. http://dx.doi.org/10.1038/nature04433.
  • Smith BC, Denu JM. 2009. Chemical mechanisms of histone lysine and arginine modifications. Biochim. Biophys. Acta 1789:45–57. http://dx.doi.org/10.1016/j.bbagrm.2008.06.005.
  • Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E, Zeitlinger J, Lewitter F, Gifford DK, Young Ra. 2005. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122:517–527. http://dx.doi.org/10.1016/j.cell.2005.06.026.
  • Li B, Carey M, Workman JL. 2007. The role of chromatin during transcription. Cell 128:707–719. http://dx.doi.org/10.1016/j.cell.2007.01.015.
  • Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39:311–318. http://dx.doi.org/10.1038/ng1966.
  • Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young Ra. 2007. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77–88. http://dx.doi.org/10.1016/j.cell.2007.05.042.
  • Chi P, Allis CD, Wang GG. 2010. Covalent histone modifications–miswritten, misinterpreted and mis-erased in human cancers. Nat. Rev. Cancer 10:457–469. http://dx.doi.org/10.1038/nrc2876.
  • Greer EL, Shi Y. 2012. Histone methylation: a dynamic mark in health, disease and inheritance. Nat. Rev. Genet. 13:343–357. http://dx.doi.org/10.1038/nrg3173.
  • Lu C, Ward PS, Kapoor GS, Rohle D, Turcan S, Abdel-Wahab O, Edwards CR, Khanin R, Figueroa ME, Melnick A, Wellen KE, O'Rourke DM, Berger SL, Chan TA, Levine RL, Mellinghoff IK, Thompson CB. 2012. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature 483:474–478. http://dx.doi.org/10.1038/nature10860.
  • Ulanovskaya OA, Zuhl AM, Cravatt BF. 2013. NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink. Nat. Chem. Biol. 9:300–306. http://dx.doi.org/10.1038/nchembio.1204.
  • Liang G, Zhang Y. 2013. Embryonic stem cell and induced pluripotent stem cell: an epigenetic perspective. Cell Res. 23:49–69. http://dx.doi.org/10.1038/cr.2012.175.
  • Ang Y-S, Tsai S-Y, Lee D-F, Monk J, Su J, Ratnakumar K, Ding J, Ge Y, Darr H, Chang B, Wang J, Rendl M, Bernstein E, Schaniel C, Lemischka IR. 2011. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145:183–197. http://dx.doi.org/10.1016/j.cell.2011.03.003.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.