Plant Molecular Biology

, Volume 74, Issue 1–2, pp 183–200 | Cite as

Histone dynamics and roles of histone acetyltransferases during cold-induced gene regulation in Arabidopsis

  • Kanchan Pavangadkar
  • Michael F. Thomashow
  • Steven J. Triezenberg


In Arabidopsis, CBF transcription factors bind to and activate certain cold-regulated (COR) gene promoters during cold acclimation. Consistent with the prevailing model that histone acetylation and nucleosomal depletion correspond with transcriptionally active genes, we now report that H3 acetylation increases and nucleosome occupancy decreases at COR gene promoters upon cold acclimation. Overexpression of CBF1 resulted in a constitutive increase in H3 acetylation and decrease in nucleosome occupancy, consistent with the constitutive activation of COR gene expression. Overexpression of a truncated form of CBF2 lacking its transcriptional activation domain resulted in a cold-stimulated increase in H3 acetylation, but no change in nucleosomal occupancy or COR gene expression, indicating that histone acetylation is congruent with but not sufficient for cold-activation of COR gene expression. Plants homozygous for T-DNA disruption alleles of GCN5 (encoding a histone acetyltransferase) or ADA2b (a GCN5-interacting protein) show diminished expression of COR genes during cold acclimation. Contrary to expectations, H3 acetylation at COR gene promoters was stimulated upon cold acclimation in ada2b and gcn5 plants as in wild type plants, but the decrease in nucleosome occupancy was diminished. Thus, GCN5 is not the HAT responsible for histone acetylation at COR gene promoters during cold acclimation. Several other HAT mutant plants were also tested; although some do affect COR gene expression, none affected histone acetylation. Therefore, H3 acetylation at the COR gene promoters is not solely dependent on any of the HATs tested.


Chromatin remodeling Histone acetyltransferase HAT GCN5 ADA2 Plant gene regulation Cold acclimation 



This research was supported by grants from the US National Science Foundation (MCB-0240309), the NSF Plant Genome Project (DBI 0110124 and DBI 0701709), the Department of Energy (DE-FG02-91ER20021) and the Michigan Agricultural Experiment Station and by the Van Andel Research Institute. We thank Drs. Kostas Vlachonasios and Amy Hark for thoughtful discussions during the course of this work, and Colleen Doherty and Sarah Gilmour for sharing plant lines and data prior to publication.


  1. Altaf M, Auger A, Monnet-Saksouk J, Brodeur J, Piquet S, Cramet M, Bouchard N, Lacoste N, Utley RT, Gaudreau L, Cote J (2010) NuA4-dependent acetylation of nucleosomal histone H4 and H2A directly stimulates incorporation of H2A.Z by the SWR1 complex. J Biol ChemGoogle Scholar
  2. Artus NN, Uemura M, Steponkus PL, Gilmour SJ, Lin C, Thomashow MF (1996) Constitutive expression of the cold-regulated Arabidopsis thaliana COR15a gene affects both chloroplast and protoplast freezing tolerance. Proc Natl Acad Sci USA 93:13404–13409CrossRefPubMedGoogle Scholar
  3. Ascenzi R, Gantt JS (1999) Subnuclear distribution of the entire complement of linker histone variants in Arabidopsis thaliana. Chromosoma 108:345–355CrossRefPubMedGoogle Scholar
  4. Auty R, Steen H, Myers LC, Persinger J, Bartholomew B, Gygi SP, Buratowski S (2004) Purification of active TFIID from Saccharomyces cerevisiae. Extensive promoter contacts and co-activator function. J Biol Chem 279:49973–49981CrossRefPubMedGoogle Scholar
  5. Baker SP, Grant PA (2007) The SAGA continues: expanding the cellular role of a transcriptional co-activator complex. Oncogene 26:5329–5340CrossRefPubMedGoogle Scholar
  6. Baker SS, Wilhelm KS, Thomashow MF (1994) The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol Biol 24:701–713CrossRefPubMedGoogle Scholar
  7. Barbaric S, Reinke H, Horz W (2003) Multiple mechanistically distinct functions of SAGA at the PHO5 promoter. Mol Cell Biol 23:3468–3476CrossRefPubMedGoogle Scholar
  8. Barlev NA, Emelyanov AV, Castagnino P, Zegerman P, Bannister AJ, Sepulveda MA, Robert F, Tora L, Kouzarides T, Birshtein BK, Berger SL (2003) A novel human Ada2 homologue functions with Gcn5 or Brg1 to coactivate transcription. Mol Cell Biol 23:6944–6957CrossRefPubMedGoogle Scholar
  9. Benhamed M, Bertrand C, Servet C, Zhou DX (2006) Arabidopsis GCN5, HD1, and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression. Plant Cell 18:2893–2903CrossRefPubMedGoogle Scholar
  10. Berger SL (2002) Histone modifications in transcriptional regulation. Curr Opin Genet Dev 12:142–148CrossRefPubMedGoogle Scholar
  11. Bertrand C, Benhamed M, Li YF, Ayadi M, Lemonnier G, Renou JP, Delarue M, Zhou DX (2005) Arabidopsis HAF2 gene encoding TATA-binding protein (TBP)-associated factor TAF1, is required to integrate light signals to regulate gene expression and growth. J Biol Chem 280:1465–1473CrossRefPubMedGoogle Scholar
  12. Bond DM, Dennis ES, Pogson BJ, Finnegan EJ (2009) Histone acetylation, VERNALIZATION INSENSITIVE 3, FLOWERING LOCUS C, and the vernalization response. Mol Plant 2:724–737CrossRefPubMedGoogle Scholar
  13. Bordoli L, Netsch M, Luthi U, Lutz W, Eckner R (2001) Plant orthologs of p300/CBP: conservation of a core domain in metazoan p300/CBP acetyltransferase-related proteins. Nucleic Acids Res 29:589–597CrossRefPubMedGoogle Scholar
  14. Candau R, Zhou JX, Allis CD, Berger SL (1997) Histone acetyltransferase activity and interaction with ADA2 are critical for GCN5 function in vivo. EMBO J 16:555–565CrossRefPubMedGoogle Scholar
  15. Canella D, Gilmour SJ, Kuhn LA, Thomashow MF (2009) DNA binding by the Arabidopsis CBF1 transcription factor requires the PKKP/RAGRxKFxETRHP signature sequence. Biochim Biophys ActaGoogle Scholar
  16. Deng W, Liu C, Pei Y, Deng X, Niu L, Cao X (2007) Involvement of the histone acetyltransferase AtHAC1 in the regulation of flowering time via repression of FLOWERING LOCUS C in Arabidopsis. Plant Physiol 143:1660–1668CrossRefPubMedGoogle Scholar
  17. Doherty CJ (2008) Transcriptional networks involved in response to low temperature stress in Arabidopsis thaliana. Thesis (Ph. D), Michgian State University, Dept. of Biochemistry and Molecular BiologyGoogle Scholar
  18. Earley KW, Shook MS, Brower-Toland B, Hicks L, Pikaard CS (2007) In vitro specificities of Arabidopsis co-activator histone acetyltransferases: implications for histone hyperacetylation in gene activation. Plant J 52:615–626CrossRefPubMedGoogle Scholar
  19. Eberharter A, Sterner DE, Schieltz D, Hassan A, Yates JR III, Berger SL, Workman JL (1999) The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae. Mol Cell Biol 19:6621–6631PubMedGoogle Scholar
  20. Gamborg OL, Eveleigh DE (1968) Culture methods and detection of glucanases in suspension cultures of wheat and barley. Can J Biochem 46:417–421CrossRefPubMedGoogle Scholar
  21. Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50:151–158CrossRefPubMedGoogle Scholar
  22. Gilmour SJ, Lin C, Thomashow MF (1996) Purification and properties of Arabidopsis thaliana COR (cold-regulated) gene polypeptides COR15am and COR6.6 expressed in Escherichia coli. Plant Physiol 111:293–299CrossRefPubMedGoogle Scholar
  23. Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF (1998) Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J 16:433–442CrossRefPubMedGoogle Scholar
  24. Gilmour SJ, Sebolt AM, Salazar MP, Everard JD, Thomashow MF (2000) Overexpression of the Arabidopsis CBF3 transcriptional activator mimics multiple biochemical changes associated with cold acclimation. Plant Physiol 124:1854–1865CrossRefPubMedGoogle Scholar
  25. Gilmour SJ, Fowler SG, Thomashow MF (2004) Arabidopsis transcriptional activators CBF1, CBF2, and CBF3 have matching functional activities. Plant Mol Biol 54:767–781CrossRefPubMedGoogle Scholar
  26. Govind CK, Zhang F, Qiu H, Hofmeyer K, Hinnebusch AG (2007) Gcn5 promotes acetylation, eviction, and methylation of nucleosomes in transcribed coding regions. Mol Cell 25:31–42CrossRefPubMedGoogle Scholar
  27. Grant PA, Duggan L, Cote J, Roberts SM, Brownell JE, Candau R, Ohba R, Owen-Hughes T, Allis CD, Winston F, Berger SL, Workman JL (1997) Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev 11:1640–1650CrossRefPubMedGoogle Scholar
  28. Grau B, Popescu C, Torroja L, Ortuno-Sahagun D, Boros I, Ferrus A (2008) Transcriptional adaptor ADA3 of Drosophila melanogaster is required for histone modification, position effect variegation, and transcription. Mol Cell Biol 28:376–385CrossRefPubMedGoogle Scholar
  29. Gu W, Roeder RG (1997) Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain. Cell 90:595–606CrossRefPubMedGoogle Scholar
  30. Hajela RK, Horvath DP, Gilmour SJ, Thomashow MF (1990) Molecular cloning and expression of cor (cold-regulated) genes in Arabidopsis thaliana. Plant Physiol 93:1246–1252CrossRefPubMedGoogle Scholar
  31. Han SK, Song JD, Noh YS, Noh B (2007) Role of plant CBP/p300-like genes in the regulation of flowering time. Plant J 49:103–114CrossRefPubMedGoogle Scholar
  32. Hark AT, Vlachonasios KE, Pavangadkar KA, Rao S, Gordon H, Adamakis ID, Kaldis A, Thomashow MF, Triezenberg SJ (2009) Two Arabidopsis orthologs of the transcriptional coactivator ADA2 have distinct biological functions. Biochim Biophys Acta 1789:117–124PubMedGoogle Scholar
  33. Herrera FJ, Triezenberg SJ (2004) VP16-dependent association of chromatin-modifying coactivators and underrepresentation of histones at immediate-early gene promoters during herpes simplex virus infection. J Virol 78:9689–9696CrossRefPubMedGoogle Scholar
  34. Hong L, Schroth GP, Matthews HR, Yau P, Bradbury EM (1993) Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA. J Biol Chem 268:305–314PubMedGoogle Scholar
  35. Horiuchi J, Silverman N, Pina B, Marcus GA, Guarente L (1997) ADA1, a novel component of the ADA/GCN5 complex, has broader effects than GCN5, ADA2, or ADA3. Mol Cell Biol 17:3220–3228PubMedGoogle Scholar
  36. Imhof A, Yang XJ, Ogryzko VV, Nakatani Y, Wolffe AP, Ge H (1997) Acetylation of general transcription factors by histone acetyltransferases. Curr Biol 7:689–692CrossRefPubMedGoogle Scholar
  37. Jaglo-Ottosen KR, Gilmour SJ, Zarka DG, Schabenberger O, Thomashow MF (1998) Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science 280:104–106CrossRefPubMedGoogle Scholar
  38. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080CrossRefPubMedGoogle Scholar
  39. Kornberg RD, Lorch Y (1999) Chromatin-modifying and -remodeling complexes. Curr Opin Genet Dev 9:148–151CrossRefPubMedGoogle Scholar
  40. Krebs JE, Kuo MH, Allis CD, Peterson CL (1999) Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. Genes Dev 13:1412–1421CrossRefPubMedGoogle Scholar
  41. Kuo MH, Allis CD (1998) Roles of histone acetyltransferases and deacetylases in gene regulation. Bioessays 20:615–626CrossRefPubMedGoogle Scholar
  42. Lee TI, Young RA (2000) Transcription of eukaryotic protein-coding genes. Annu Rev Genet 34:77–137CrossRefPubMedGoogle Scholar
  43. Lee DY, Hayes JJ, Pruss D, Wolffe AP (1993) A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell 72:73–84CrossRefPubMedGoogle Scholar
  44. Loidl P (1994) Histone acetylation: facts and questions. Chromosoma 103:441–449CrossRefPubMedGoogle Scholar
  45. Mao Y, Pavangadkar KA, Thomashow MF, Triezenberg SJ (2006) Physical and functional interactions of Arabidopsis ADA2 transcriptional coactivator proteins with the acetyltransferase GCN5 and with the cold-induced transcription factor CBF1. Biochim Biophys Acta 1759:69–79PubMedGoogle Scholar
  46. Martinez E, Kundu TK, Fu J, Roeder RG (1998) A human SPT3-TAFII31-GCN5-L acetylase complex distinct from transcription factor IID. J Biol Chem 273:23781–23785CrossRefPubMedGoogle Scholar
  47. Meng G, Zhao Y, Nag A, Zeng M, Dimri G, Gao Q, Wazer DE, Kumar R, Band H, Band V (2004) Human ADA3 binds to estrogen receptor (ER) and functions as a coactivator for ER-mediated transactivation. J Biol Chem 279:54230–54240CrossRefPubMedGoogle Scholar
  48. Nag A, Germaniuk-Kurowska A, Dimri M, Sassack MA, Gurumurthy CB, Gao Q, Dimri G, Band H, Band V (2007) An essential role of human Ada3 in p53 acetylation. J Biol Chem 282:8812–8820CrossRefPubMedGoogle Scholar
  49. Nagy Z, Riss A, Romier C, le Guezennec X, Dongre AR, Orpinell M, Han J, Stunnenberg H, Tora L (2009) The human SPT20-containing SAGA complex plays a direct role in the regulation of endoplasmic reticulum stress-induced genes. Mol Cell Biol 29:1649–1660CrossRefPubMedGoogle Scholar
  50. Novillo F, Medina J, Salinas J (2007) Arabidopsis CBF1 and CBF3 have a different function than CBF2 in cold acclimation and define different gene classes in the CBF regulon. Proc Natl Acad Sci USA 104:21002–21007CrossRefPubMedGoogle Scholar
  51. Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30:5036–5055CrossRefPubMedGoogle Scholar
  52. Pina B, Berger S, Marcus GA, Silverman N, Agapite J, Guarente L (1993) ADA3: a gene, identified by resistance to GAL4-VP16, with properties similar to and different from those of ADA2. Mol Cell Biol 13:5981–5989PubMedGoogle Scholar
  53. Pray-Grant MG, Schieltz D, McMahon SJ, Wood JM, Kennedy EL, Cook RG, Workman JL, Yates JR III, Grant PA (2002) The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway. Mol Cell Biol 22:8774–8786CrossRefPubMedGoogle Scholar
  54. Qi D, Larsson J, Mannervik M (2004) Drosophila Ada2b is required for viability and normal histone H3 acetylation. Mol Cell Biol 24:8080–8089CrossRefPubMedGoogle Scholar
  55. Reinke H, Gregory PD, Horz W (2001) A transient histone hyperacetylation signal marks nucleosomes for remodeling at the PHO8 promoter in vivo. Mol Cell 7:529–538CrossRefPubMedGoogle Scholar
  56. Roth SY, Denu JM, Allis CD (2001) Histone acetyltransferases. Annu Rev Biochem 70:81–120CrossRefPubMedGoogle Scholar
  57. Sendra R, Tse C, Hansen JC (2000) The yeast histone acetyltransferase A2 complex, but not free Gcn5p, binds stably to nucleosomal arrays. J Biol Chem 275:24928–24934CrossRefPubMedGoogle Scholar
  58. Shinwari ZK, Nakashima K, Miura S, Kasuga M, Seki M, Yamaguchi-Shinozaki K, Shinozaki K (1998) An Arabidopsis gene family encoding DRE/CRT binding proteins involved in low-temperature-responsive gene expression. Biochem Biophys Res Commun 250:161–170CrossRefPubMedGoogle Scholar
  59. Sterner DE, Grant PA, Roberts SM, Duggan LJ, Belotserkovskaya R, Pacella LA, Winston F, Workman JL, Berger SL (1999) Functional organization of the yeast SAGA complex: distinct components involved in structural integrity, nucleosome acetylation, and TATA-binding protein interaction. Mol Cell Biol 19:86–98PubMedGoogle Scholar
  60. Sterner DE, Belotserkovskaya R, Berger SL (2002a) SALSA, a variant of yeast SAGA, contains truncated Spt7, which correlates with activated transcription. Proc Natl Acad Sci USA 99:11622–11627CrossRefPubMedGoogle Scholar
  61. Sterner DE, Wang X, Bloom MH, Simon GM, Berger SL (2002b) The SANT domain of Ada2 is required for normal acetylation of histones by the yeast SAGA complex. J Biol Chem 277:8178–8186CrossRefPubMedGoogle Scholar
  62. Stockinger EJ, Gilmour SJ, Thomashow MF (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci USA 94:1035–1040CrossRefPubMedGoogle Scholar
  63. Stockinger EJ, Mao Y, Regier MK, Triezenberg SJ, Thomashow MF (2001) Transcriptional adaptor and histone acetyltransferase proteins in Arabidopsis and their interactions with CBF1, a transcriptional activator involved in cold-regulated gene expression. Nucleic Acids Res 29:1524–1533CrossRefPubMedGoogle Scholar
  64. Syntichaki P, Topalidou I, Thireos G (2000) The Gcn5 bromodomain co-ordinates nucleosome remodelling. Nature 404:414–417CrossRefPubMedGoogle Scholar
  65. Thomashow MF (2001) So what’s new in the field of plant cold acclimation? Lots!. Plant Physiol 125:89–93CrossRefPubMedGoogle Scholar
  66. Timmers HT, Tora L (2005) SAGA unveiled. Trends Biochem Sci 30:7–10CrossRefPubMedGoogle Scholar
  67. Triezenberg SJ (1995) Structure and function of transcriptional activation domains. Curr Opin Genet Dev 5:190–196CrossRefPubMedGoogle Scholar
  68. Turner BM, O’Neill LP (1995) Histone acetylation in chromatin and chromosomes. Semin Cell Biol 6:229–236CrossRefPubMedGoogle Scholar
  69. Vettese-Dadey M, Walter P, Chen H, Juan LJ, Workman JL (1994) Role of the histone amino termini in facilitated binding of a transcription factor, GAL4-AH, to nucleosome cores. Mol Cell Biol 14:970–981PubMedGoogle Scholar
  70. Vlachonasios KE, Thomashow MF, Triezenberg SJ (2003) Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development, and gene expression. Plant Cell 15:626–638CrossRefPubMedGoogle Scholar
  71. Wade PA, Pruss D, Wolffe AP (1997) Histone acetylation: chromatin in action. Trends Biochem Sci 22:128–132CrossRefPubMedGoogle Scholar
  72. Wang Z, Triezenberg SJ, Thomashow MF, Stockinger EJ (2005) Multiple hydrophobic motifs in Arabidopsis CBF1 COOH-terminus provide functional redundancy in trans-activation. Plant Mol Biol 58:543–559CrossRefPubMedGoogle Scholar
  73. Wassarman DA, Sauer F (2001) TAF(II)250: a transcription toolbox. J Cell Sci 114:2895–2902PubMedGoogle Scholar
  74. Workman JL, Kingston RE (1998) Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem 67:545–579CrossRefPubMedGoogle Scholar
  75. Yamaguchi-Shinozaki K, Shinozaki K (1994) A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6:251–264CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Kanchan Pavangadkar
    • 1
    • 2
  • Michael F. Thomashow
    • 1
    • 2
    • 3
  • Steven J. Triezenberg
    • 1
    • 4
    • 5
  1. 1.Graduate Program in GeneticsMichigan State UniversityEast LansingUSA
  2. 2.Department of Microbiology and Molecular GeneticsMichigan State UniversityEast LansingUSA
  3. 3.MSU-DOE Plant Research LaboratoryMichigan State UniversityEast LansingUSA
  4. 4.Department of Biochemistry and Molecular GeneticsMichigan State UniversityEast LansingUSA
  5. 5.Van Andel Research InstituteGrand RapidsUSA

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