Correction: Promoter-bound p300 complexes facilitate post-mitotic transmission of transcriptional memory (PLoS ONE (2014) 9, 6 (e99989) DOI: 10.1371/journal.pone.0099989);Promoter-bound p300 complexes facilitate post-mitotic transmission of transcriptional memory

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Wong, Madeline M ^a   Byun, Jung S ^a   Sacta, Maria ^a   Jin, Qihuang ^b   Baek, SongJoon ^a   Gardner, Kevin ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; E1A ASSOCIATED P300 PROTEIN; MEDIATOR COMPLEX; RNA POLYMERASE II; TATA BINDING PROTEIN ASSOCIATED FACTOR; BRD4 PROTEIN, HUMAN; CELL CYCLE PROTEIN; CHROMATIN; COHESIN; EP300 PROTEIN, HUMAN; HISTONE; NONHISTONE PROTEIN; NUCLEAR PROTEIN; PROTEIN BINDING; TATA BINDING PROTEIN; TBP PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

ANIMAL CELL; ARTICLE; CELL DIFFERENTIATION; CELL FATE; CHROMATIN; CONTROLLED STUDY; GENE ACTIVATION; GENE EXPRESSION; GENE INTERACTION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; MITOSIS; MOUSE; NONHUMAN; POST MITOTIC TRANSMISSION; PREINITIATION COMPLEX; PROTEIN ASSEMBLY; PROTEIN FUNCTION; TRANSCRIPTION INITIATION; TRANSCRIPTIONAL MEMORY; CELL PROLIFERATION; CHEMISTRY; CHROMATIN ASSEMBLY AND DISASSEMBLY; DEFICIENCY; GENE INACTIVATION; GENETIC EPIGENESIS; GENETICS; HCT116 CELL LINE; INHERITANCE; JURKAT CELL LINE; METABOLISM; PROMOTER REGION; SIGNAL TRANSDUCTION;

CELL CYCLE PROTEINS; CELL PROLIFERATION; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOMAL PROTEINS, NON-HISTONE; E1A-ASSOCIATED P300 PROTEIN; EPIGENESIS, GENETIC; GENE KNOCKOUT TECHNIQUES; HCT116 CELLS; HISTONES; HUMANS; INHERITANCE PATTERNS; JURKAT CELLS; MEDIATOR COMPLEX; MITOSIS; NUCLEAR PROTEINS; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; RNA POLYMERASE II; SIGNAL TRANSDUCTION; TATA-BOX BINDING PROTEIN; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84903388658     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0106126     Document Type: Erratum

References (83)

1. Delcuve GP, Rastegar M, Davie JR (2009) Epigenetic control. J Cell Physiol 219: 243-250.
2. Sarge KD, Park-Sarge OK (2009) Mitotic bookmarking of formerly active genes: keeping epigenetic memories from fading. Cell Cycle 8: 818-823.
3. Ng RK, Gurdon JB (2008) Epigenetic memory of an active gene state depends on histone H3.3 incorporation into chromatin in the absence of transcription. Nat Cell Biol 10: 102-109.
4. Christova R, Oelgeschlager T (2002) Association of human TFIID-promoter complexes with silenced mitotic chromatin in vivo. Nat Cell Biol 4: 79-82. (Pubitemid 34071984)
5. Young DW, Hassan MQ, Yang XQ, Galindo M, Javed A, et al. (2007) Mitotic retention of gene expression patterns by the cell fate-determining transcription factor Runx2. Proc Natl Acad Sci U S A 104: 3189-3194. (Pubitemid 46364135)
6. Xing H, Wilkerson DC, Mayhew CN, Lubert EJ, Skaggs HS, et al. (2005) Mechanism of hsp70i gene bookmarking. Science 307: 421-423. (Pubitemid 40139986)
7. Xing H, Vanderford NL, Sarge KD (2008) The TBP-PP2A mitotic complex bookmarks genes by preventing condensin action. Nat Cell Biol 10: 1318-1323.
8. Kadauke S, Udugama MI, Pawlicki JM, Achtman JC, Jain DP, et al. (2012) Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1. Cell 150: 725-737. S0092-8674(12)00881-1 [pii]; 10.1016/j.cell.2012.06.038 [doi].
9. Caravaca JM, Donahue G, Becker JS, He X, Vinson C, et al. (2013) Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes. Genes Dev 27: 251-260. gad.206458.112 [pii]; 10.1101/gad.206458.112 [doi].
10. Groudine M, Weintraub H (1982) Propagation of globin DNAase I-hypersensitive sites in absence of factors required for induction: a possible mechanism for determination. Cell 30: 131-139. (Pubitemid 13237092)
11. Zhao R, Nakamura T, Fu Y, Lazar Z, Spector DL (2011) Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nat Cell Biol 13: 1295-1304. ncb2341 [pii]; 10.1038/ncb2341 [doi].
12. Dey A, Nishiyama A, Karpova T, McNally J, Ozato K (2009) Brd4 Marks Select Genes on Mitotic Chromatin and Directs Post-mitotic Transcription. Mol Biol Cell.
13. Blobel GA, Kadauke S, Wang E, Lau AW, Zuber J, et al. (2009) A reconfigured pattern of MLL occupancy within mitotic chromatin promotes rapid transcriptional reactivation following mitotic exit. Mol Cell 36: 970-983. S1097-2765(09)00904-6 [pii]; 10.1016/j.molcel.2009.12.001 [doi].
14. John S, Workman JL (1998) Bookmarking genes for activation in condensed mitotic chromosomes. Bioessays 20: 275-279. (Pubitemid 28205542)
15. Kadauke S, Blobel GA (2013) Mitotic bookmarking by transcription factors. Epigenetics Chromatin 6: 6. 1756-8935-6-6 [pii]; 10.1186/1756-8935-6-6 [doi].
16. Zaidi SK, Young DW, Montecino MA, Lian JB, van Wijnen AJ, et al. (2010) Mitotic bookmarking of genes: a novel dimension to epigenetic control. Nat Rev Genet 11: 583-589. nrg2827 [pii]; 10.1038/nrg2827 [doi].
17. Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, et al. (2007) RNA polymerase is poised for activation across the genome. Nat Genet 39: 1507-1511. (Pubitemid 350191341)
18. Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, et al. (2007) RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 39: 1512-1516. (Pubitemid 350191345)
19. Kininis M, Isaacs GD, Core LJ, Hah N, Kraus WL (2009) Postrecruitment regulation of RNA polymerase II directs rapid signaling responses at the promoters of estrogen target genes. Mol Cell Biol 29: 1123-1133.
20. Byun JS, Wong MM, Cui W, Idelman G, Li Q, et al. (2009) Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes. Proc Natl Acad Sci U S A 106: 19286-19291.
21. Sheng M, McFadden G, Greenberg ME (1990) Membrane depolarization and calcium induce c-fos transcription via phosphorylation of transcription factor CREB. Neuron 4: 571-582. (Pubitemid 20160846)
22. Ganusov VV, Pilyugin SS, de Boer RJ, Murali-Krishna K, Ahmed R, et al. (2005) Quantifying cell turnover using CFSE data. J Immunol Methods 298: 183-200. S0022-1759(05)00025-6 [pii]; 10.1016/j.jim.2005.01.011 [doi].
23. Yang M, Zhang Z, Wang C, Li K, Li S, et al. (2012) Nesfatin-1 action in the brain increases insulin sensitivity through Akt/AMPK/TORC2 pathway in diet-induced insulin resistance. Diabetes 61: 1959-1968. db11-1755 [pii]; 10.2337/db11-1755 [doi].
24. Ge Y, Montano I, Rustici G, Freebern WJ, Haggerty CM, et al. (2006) Selective leukemic-cell killing by a novel functional class of thalidomide analogs. Blood 108: 4126-4135. (Pubitemid 44913284)
25. Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, et al. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 13: 1977-2000. (Pubitemid 34651487)
26. O'Donnell A, Odrowaz Z, Sharrocks AD (2012) Immediate-early gene activation by the MAPK pathways: what do and don't we know? Biochem Soc Trans 40: 58-66. BST20110636 [pii]; 10.1042/BST20110636 [doi].
27. Yang SH, Jaffray E, Hay RT, Sharrocks AD (2003) Dynamic interplay of the SUMO and ERK pathways in regulating Elk-1 transcriptional activity. Mol Cell 12: 63-74. S109727650300265X [pii].
28. Crump NT, Hazzalin CA, Bowers EM, Alani RM, Cole PA, et al. (2011) Dynamic acetylation of all lysine-4 trimethylated histone H3 is evolutionarily conserved and mediated by p300/CBP. Proc Natl Acad Sci U S A 108: 7814-7819. 1100099108 [pii]; 10.1073/pnas.1100099108 [doi].
29. Li QJ, Yang SH, Maeda Y, Sladek FM, Sharrocks AD, et al. (2003) MAP kinase phosphorylation-dependent activation of Elk-1 leads to activation of the coactivator p300. EMBO J 22: 281-291. 10.1093/emboj/cdg028 [doi]. (Pubitemid 36119434)
30. Chrivia JC, Kwok RP, Lamb N, Hagiwara M, Montminy MR, et al. (1993) Phosphorylated CREB binds specifically to the nuclear protein CBP. Nature 365: 855-859. (Pubitemid 23341031)
31. Parker D, Ferreri K, Nakajima T, LaMorte VJ, Evans R, et al. (1996) Phosphorylation of CREB at Ser-133 induces complex formation with CREB-binding protein via a direct mechanism. Mol Cell Biol 16: 694-703.
32. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465: 182-187. nature09033 [pii]; 10.1038/nature09033 [doi].
33. Remeseiro S, Losada A (2013) Cohesin, a chromatin engagement ring. Curr Opin Cell Biol 25: 63-71. S0955-0674(12)00176-7 [pii]; 10.1016/j.ceb.2012.10.013 [doi].
34. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, et al. (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467: 430-435. nature09380 [pii]; 10.1038/nature09380 [doi].
35. Cuylen S, Haering CH (2010) A new cohesive team to mediate DNA looping. Cell Stem Cell 7: 424-426. S1934-5909(10)00449-2 [pii]; 10.1016/j.stem.2010.09. 006 [doi].
36. Martinez-Balbas MA, Dey A, Rabindran SK, Ozato K, Wu C (1995) Displacement of sequence-specific transcription factors from mitotic chromatin. Cell 83: 29-38.
37. Kruhlak MJ, Hendzel MJ, Fischle W, Bertos NR, Hameed S, et al. (2001) Regulation of global acetylation in mitosis through loss of histone acetyltransferases and deacetylases from chromatin. J Biol Chem 276: 38307-38319.
38. Zaidi SK, Young DW, Pockwinse SM, Javed A, Lian JB, et al.(2003) Mitotic partitioning and selective reorganization of tissue-specific transcription factors in progeny cells. Proc Natl Acad Sci U S A 100: 14852-14857. (Pubitemid 37517980)
39. Krubasik D, Iyer NG, English WR, Ahmed AA, Vias M, et al. (2006) Absence of p300 induces cellular phenotypic changes characteristic of epithelial to mesenchyme transition. Br J Cancer 94: 1326-1332.
40. Cosenza SC, Yumet G, Soprano DR, Soprano KJ (1994) Induction of c-fos and c-jun mRNA at the M/G1 border is required for cell cycle progression. J Cell Biochem 55: 503-512. (Pubitemid 24268154)
41. Butscher WG, Powers C, Olive M, Vinson C, Gardner K (1998) Coordinate transactivation of the interleukin-2 CD28 response element by c-Rel and ATF-1/CREB2. J Biol Chem 273: 552-560. (Pubitemid 28042244)
42. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, et al. (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8: e1000384. 10.1371/journal.pbio.1000384 [doi].
43. Schaaf CA, Kwak H, Koenig A, Misulovin Z, Gohara DW, et al. (2013) Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet 9: e1003382. 10.1371/journal.pgen.1003382 [doi]; PGENETICS-D-12-02409 [pii].
44. Huang ZQ, Li J, Sachs LM, Cole PA, Wong J (2003) A role for cofactor-cofactor and cofactor-histone interactions in targeting p300, SWI/SNF and Mediator for transcription. EMBO J 22: 2146-2155. 10.1093/emboj/cdg219 [doi]. (Pubitemid 36565538)
45. Acevedo ML, Kraus WL (2003) Mediator and p300/CBP-steroid receptor coactivator complexes have distinct roles, but function synergistically, during estrogen receptor alpha-dependent transcription with chromatin templates. Mol Cell Biol 23: 335-348. (Pubitemid 36008524)
46. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854-858. nature07730 [pii]; 10.1038/nature07730 [doi].
47. Jang MK, Mochizuki K, Zhou M, Jeong HS, Brady JN, et al. (2005) The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Mol Cell 19: 523-534. S1097-2765(05)01432-2 [pii]; 10.1016/j.molcel.2005.06.027 [doi].
48. Yang Z, Yik JH, Chen R, He N, Jang MK, et al. (2005) Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol Cell 19: 535-545. (Pubitemid 41140010)
49. Goodman RH, Smolik S (2000) CBP/p300 in cell growth, transformation, and development. Genes Dev 14: 1553-1577. (Pubitemid 30460905)
50. Bedford DC, Kasper LH, Fukuyama T, Brindle PK (2010) Target gene context influences the transcriptional requirement for the KAT3 family of CBP and p300 histone acetyltransferases. Epigenetics 5: 9-15. 10449 [pii].
51. Wang F, Marshall CB, Ikura M (2013) Transcriptional/epigenetic regulator CBP/p300 in tumorigenesis: structural and functional versatility in target recognition. Cell Mol Life Sci. 10.1007/s00018-012-1254-4 [doi].
52. Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, et al. (2010) Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 20: 565-577. gr.104471.109 [pii]; 10.1101/gr.104471.109 [doi].
53. Schiltz RL, Mizzen CA, Vassilev A, Cook RG, Allis CD, et al. (1999) Overlapping but distinct patterns of histone acetylation by the human coactivators p300 and PCAF within nucleosomal substrates. J Biol Chem 274: 1189-1192.
54. Sunagawa Y, Morimoto T, Takaya T, Kaichi S, Wada H, et al. (2010) Cyclin-dependent kinase-9 is a component of the p300/GATA4 complex required for phenylephrine-induced hypertrophy in cardiomyocytes. J Biol Chem 285: 9556-9568. M109.070458 [pii]; 10.1074/jbc.M109.070458 [doi].
55. Byun JS, Fufa TD, Wakano C, Fernandez A, Haggerty CM, et al. (2012) ELL facilitates RNA polymerase II pause site entry and release. Nat Commun 3: 633. ncomms1652 [pii]; 10.1038/ncomms1652 [doi].
56. Jin Q, Yu LR, Wang L, Zhang Z, Kasper LH, et al. (2011) Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO J 30: 249-262. emboj2010318 [pii]; 10.1038/emboj.2010.318 [doi].
57. Smallwood A, Ren B (2013) Genome organization and long-range regulation of gene expression by enhancers. Curr Opin Cell Biol. S0955-0674(13)00028-8 [pii]; 10.1016/j.ceb.2013.02.005 [doi].
58. Prescott DM, Bender M (1962) Synthesis of RNA and protein during mitosis in mammalian tissue culture cells. Exp Cell Res 26: 260-268.
59. Parsons GG, Spencer CA (1997) Mitotic repression of RNA polymerase II transcription is accompanied by release of transcription elongation complexes. Mol Cell Biol 17: 5791-5802. (Pubitemid 27411086)
60. Prasanth KV, Sacco-Bubulya PA, Prasanth SG, Spector DL (2003) Sequential entry of components of the gene expression machinery into daughter nuclei. Mol Biol Cell 14: 1043-1057. (Pubitemid 36337451)
61. Kouskouti A, Talianidis I (2005) Histone modifications defining active genes persist after transcriptional and mitotic inactivation. EMBO J 24: 347-357. (Pubitemid 40216139)
62. Chen D, Dundr M, Wang C, Leung A, Lamond A, et al. (2005) Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins. J Cell Biol 168: 41-54. (Pubitemid 40111056)
63. Ali SA, Zaidi SK, Dacwag CS, Salma N, Young DW, et al. (2008) Phenotypic transcription factors epigenetically mediate cell growth control. Proc Natl Acad Sci U S A 105: 6632-6637. (Pubitemid 351754558)
64. Zaidi SK, Young DW, Montecino M, van Wijnen AJ, Stein JL, et al. (2011) Bookmarking the genome: maintenance of epigenetic information. J Biol Chem 286: 18355-18361. R110.197061 [pii]; 10.1074/jbc.R110.197061 [doi].
65. Young DW, Hassan MQ, Pratap J, Galindo M, Zaidi SK, et al. (2007) Mitotic occupancy and lineage-specific transcriptional control of rRNA genes by Runx2. Nature 445: 442-446. (Pubitemid 46160913)
66. Abraham SE, Lobo S, Yaciuk P, Wang HG, Moran E (1993) p300, and p300-associated proteins, are components of TATA-binding protein (TBP) complexes. Oncogene 8: 1639-1647. (Pubitemid 23189061)
67. Dallas PB, Yaciuk P, Moran E (1997) Characterization of monoclonal antibodies raised against p300: both p300 and CBP are present in intracellular TBP complexes. J Virol 71: 1726-1731. (Pubitemid 27030357)
68. Nakajima T, Uchida C, Anderson SF, Lee CG, Hurwitz J, et al. (1997) RNA helicase A mediates association of CBP with RNA polymerase II. Cell 90: 1107-1112.
69. von MA, Zhang S, Montminy M, Tan EM, Hemmerich P (2000) CREB-binding protein (CBP)/p300 and RNA polymerase II colocalize in transcriptionally active domains in the nucleus. J Cell Biol 150: 265-273.
70. Ferreri K, Gill G, Montminy M (1994) The cAMP-regulated transcription factor CREB interacts with a component of the TFIID complex. Proc Natl Acad Sci U S A 91: 1210-1213. (Pubitemid 24058979)
71. Moriniere J, Rousseaux S, Steuerwald U, Soler-Lopez M, Curtet S, et al. (2009) Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. Nature 461: 664-668.
72. Hasan S, Hassa PO, Imhof R, Hottiger MO (2001) Transcription coactivator p300 binds PCNA and may have a role in DNA repair synthesis. Nature 410: 387-391. 10.1038/35066610 [doi]; 35066610 [pii].
73. Liu X, Bushnell DA, Kornberg RD (2013) RNA polymerase II transcription: structure and mechanism. Biochim Biophys Acta 1829: 2-8. S1874-9399(12)00163-0 [pii]; 10.1016/j.bbagrm.2012.09.003 [doi].
74. Sekinger EA, Gross DS (2001) Silenced chromatin is permissive to activator binding and PIC recruitment. Cell 105: 403-414. (Pubitemid 32455346)
75. Azvolinsky A, Giresi PG, Lieb JD, Zakian VA (2009) Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Mol Cell 34: 722-734.
76. Chopra VS, Cande J, Hong JW, Levine M (2009) Stalled Hox promoters as chromosomal boundaries. Genes Dev 23: 1505-1509.
77. Lanzuolo C, Orlando V (2012) Memories from the polycomb group proteins. Annu Rev Genet 46: 561-589. 10.1146/annurev-genet-110711-155603 [doi].
78. Simon JA, Kingston RE (2013) Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol Cell 49: 808-824. S1097-2765(13)00141-X [pii]; 10.1016/j.molcel. 2013.02.013 [doi].
79. Barrett RM, Malvaez M, Kramar E, Matheos DP, Arrizon A, et al. (2011) Hippocampal focal knockout of CBP affects specific histone modifications, long-term potentiation, and long-term memory. Neuropsychopharmacology 36: 1545-1556. npp201161 [pii]; 10.1038/npp.2011.61 [doi].
80. Giralt A, Puigdellivol M, Carreton O, Paoletti P, Valero J, et al. (2012) Long-term memory deficits in Huntington's disease are associated with reduced CBP histone acetylase activity. Hum Mol Genet 21: 1203-1216. ddr552 [pii]; 10.1093/hmg/ddr552 [doi].
81. Maddox SA, Watts CS, Schafe GE (2013) p300/CBP histone acetyltransferase activity is required for newly acquired and reactivated fear memories in the lateral amygdala. Learn Mem 20: 109-119. 20/2/109 [pii]; 10.1101/lm.029157.112 [doi].
82. Di LJ, Byun JS, Wong MM, Wakano C, Taylor T, et al. (2013) Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer. Nat Commun 4: 1449. ncomms2438 [pii]; 10.1038/ncomms2438 [doi].
83. Hakim O, John S, Ling JQ, Biddie SC, Hoffman AR, et al. (2009) Glucocorticoid receptor activation of the Ciz1-Lcn2 locus by long range interactions. J Biol Chem 284: 6048-6052. C800212200 [pii]; 10.1074/jbc. C800212200 [doi].