Erratum: NF-Y substitutes H2A-H2B on active cell-cycle promoters: Recruitment of CoREST-KDM1 and fine-tuning of H3 methylations (Nucleic Acids Research (2008) 36 (6592-6607) DOI: 10.1093/nar/gkn699);NF-Y substitutes H2A-H2B on active cell-cycle promoters: Recruitment of CoREST-KDM1 and fine-tuning of H3 methylations

Nucleic Acids Research

Volumn 36, Issue 20, 2008, Pages 6592-6607

  Gatta, Raffaella ^a   Mantovani, Roberto ^a  

^a UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

HETERODIMER; HISTONE; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; NUCLEAR FACTOR Y; SMALL INTERFERING RNA; TRANYLCYPROMINE;

ARTICLE; CELL CYCLE G2 PHASE; CELL CYCLE M PHASE; CELL CYCLE REGULATION; CELL FREE SYSTEM; CONTROLLED STUDY; DNA MODIFICATION; ENZYME ACTIVITY; GENE INACTIVATION; GENE INTERACTION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN METHYLATION;

EID: 56649097577     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt723     Document Type: Erratum

References (83)

1. Luger,K. (2004) Structure and dynamic behavior of nucleosomes. Curr. Opin. Genet. Dev., 13, 127-135.
2. Berger,S.L. (2007) The complex language of chromatin regulation during transcription. Nature, 447, 407-412.
3. Kouzarides,T. (2007) Chromatin modifications and their function. Cell 128, 693-705.
4. Li,B., Carey,M. and Workman,J.L. (2007) The role of chromatin during trnascription. Cell, 128, 707-719.
5. Nightingale,K.P., O'Neill,L.P. and Turner,B.M. (2006) Histone modifications: Signalling receptors and potential elements of a heritable epigenetic code. Curr. Opin. Genet. Dev., 16, 125-136.
6. Ruthenburg,A.J., Allis,C.D. and Wysocka,J. (2007) Methylation of lysine 4 on histone H3: Intricacy of writing and reading a single epigenetic mark. Mol. Cell, 25, 15-30.
7. Schübeler,D., MacAlpine,D.M., Scalzo,D., Wirbelauer,C., Kooperberg,C., van Leeuwen,F., Gottschling,D.E., O'Neill,L.P., Turner,B.M., Delrow,J. et al. (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev., 18, 1263-1271.
8. Bernstein,B.E., Kamal,M., Lindblad-Toh,K., Bekiranov,S., Bailey,D.K., Huebert,D.J., McMahon,S., Karlsson,E.K., Kulbokas,E.J. III, Gingeras,T.R. et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell, 120, 169-181.
9. Hyland,E.M., Cosgrove,M.S., Molina,H., Wang,D., Pandey,A., Cottee,R.J. and Boeke,J.D. (2005) Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Mol. Cell. Biol., 25, 10060-10070.
10. Pokholok,D.K., Harbison,C.T., Levine,S., Cole,M., Hannett,N.M., Lee,T.I., Bell,G.W., Walker,K., Rolfe,P.A., Herbolsheimer,E. et al. (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell, 122, 517-527.
11. Heintzman,N.D., Stuart,R.K., Hon,G., Fu,Y., Ching,C.W., Hawkins,R.D., Barrera,L.O., Van Calcar,S., Qu,C., Ching,K.A. et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet., 39 311-318.
12. Koch,C.M., Andrews,R.M., Flicek,P., Dillon,S.C., Karaöz,U., Clelland,G.K., Wilcox,S., Beare,D.M., Fowler,J.C., Couttet,P. et al. (2007) The landscape of histone modi.cations across 1% of the human genome in five human cell lines. Genome Res., 17, 691-707.
13. Barski,A., Cuddapah,S., Cui,K., Roh,T.Y., Schones,D.E., Wang,Z., Wei,G., Chepelev,I. and Zhao,K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
14. Guenther,M.G., Levine,S.S., Boyer,L.A., Jaenisch,R. and Young,R.A. (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell, 130, 77-88.
15. Mikkelsen,T.S., Ku,M., Ja.e,D.B., Issac,B., Lieberman,E., Giannoukos,G., Alvarez,P., Brockman,W., Kim,T.K., Koche,R.P. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560.
16. Shi,Y., Lan,F., Matson,C., Mulligan,P., Whetstine,J.R., Cole,P.A., Casero,R.A. and Shi,Y. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell, 119, 941-953.
17. Forneris,F., Binda,C., Battaglioli,E. and Mattevi,A. (2008) LSD1: oxidative chemistry for multifaceted functions in chromatin regulation. Trends Biochem. Sci., 33, 181-189.
18. Christensen,J., Agger,K., Cloos,P.A., Pasini,D., Rose,S., Sennels,L., Rappsilber,J., Hansen,K.H., Salcini,A.E. and Helin,K. (2007) RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell, 128, 1063-1076.
19. Klose,R.J., Yan,Q., Tothova,Z., Yamane,K., Erdjument-Bromage,H., Tempst,P., Gilliland,D.G., Zhang,Y. and Kaelin,W.G. Jr. (2007) The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell, 128, 889-900.
20. Yamane,K., Tateishi,K., Klose,R.J., Fang,J., Fabrizio,L.A., Erdjument-Bromage,H., Taylor-Papadimitriou,J., Tempst,P. and Zhang,Y. (2007) PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol. Cell, 25 801-812.
21. Iwase,S., Lan,F., Bayliss,P., de la Torre-Ubieta,L., Huarte,M., Qi,H.H., Whetstine,J.R., Bonni,A., Roberts,T.M. and Shi,Y. (2007) The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell, 128, 1077-1088.
22. Cloos,P.A., Christensen,J., Agger,K. and Helin,K. (2008) Erasing the methyl mark: Histone demethylases at the center of cellular differentiation and disease. Genes Dev., 22, 1115-1140.
23. Cosgrove,M.S., Boeke,J.D. and Wolberger,C. (2004) Regulated nucleosome mobility and the histone code. Nat. Struct. Mol. Biol., 11, 1037-1043.
24. Kamada,K., Shu,F., Chen,H., Malik,S., Stelzer,G., Roeder,R.G., Meisterernst,M. and Burley,S.K. (2001) Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex. Cell, 106, 71-81.
25. Werten,S., Mitschler,A., Romier,C., Ganglo.,Y.G., Thuault,S., Davidson,I. and Moras,D. (2002) Crystal structure of a subcomplex of human transcription factor TFIID formed by TATA binding protein-associated factors hTAF4 (hTAF(II)135) and hTAF12 (hTAF(II)20). J. Biol. Chem., 277, 45502-45509.
26. Gangloff,Y.G., Romier,C., Thuault,S., Werten,S. and Davidson,I. (2001) The histone fold is a key structural motif of transcription factor TFIID. Trends Biochem. Sci., 26, 250-257.
27. Hartlepp,K.F., Fernández-Tornero,C., Eberharter,A., Grüne,T., Müller,C.W. and Becker,P.B. (2005) The histone fold subunits of Drosophila CHRAC facilitate nucleosome sliding through dynamic DNA interactions. Mol. Cell Biol., 25, 9886-9896.
28. Mantovani,R. (1999) The molecular biology of the CCAAT-binding factor NF-Y. Gene, 239, 15-27.
29. Romier,C., Cocchiarella,F., Mantovani,R. and Moras,D. (2003) The crystal structure of the NF-YB/NF-YC heterodimer gives insight into transcription regulation and DNA binding and bending by transcription factor NF-Y. J. Biol. Chem., 278, 1336-1345.
30. Suzuki,Y., Yamashita,R., Shirota,M., Sakakibara,Y., Chiba,J., Mizushima-Sugano,J., Nakai,K. and Sugano,S. (2004) Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Genome Res., 14, 1711-1718.
31. Zhu,Z., Shendure,J. and Church,G.M. (2005) Discovering functional transcription-factor combinations in the human cell cycle. Genome Res., 15, 848-855.
32. Grskovic,M., Chaivorapol,C., Gaspar-Maia,A., Li,H. and Ramalho-Santos,M (2007) Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells. PLoS Genet., 3, e145.
33. Lee,J., Li,Z., Brower-Sinning,R. and John,B. (2007) Regulatory circuit of human microRNA biogenesis. PLoS Comput. Biol., 3, e67.
34. Bhattacharya,A., Deng,J.M., Zhang,Z., Behringer,R., de Crombrugghe,B. and Maity,S.N. (2003) The B subunit of the CCAAT box binding transcription factor complex (CBF/NF-Y) is essential for early mouse development and cell proliferation. Cancer Res., 63, 8167-8172.
35. Elkon,R., Linhart,C., Sharan,R., Shamir,R. and Shiloh,Y. (2003) Genome-wide in silico identification of Transcriptional regulators controlling the cell cycle in human cells. Genome Res., 13, 773-780.
36. Hu,Q., Lu,J.F., Luo,R., Sen,S. and Maity,S.N. (2006) Inhibition of CBF/ NF-Y mediated transcription activation arrests cells at G2/M phase and suppresses expression of genes activated at G2/M phase of the cell cycle. Nucleic Acids Res., 34, 6272-6285.
37. Benatti,P., Basile,V., Merico,D., Fantoni,L.I., Tagliafico,E. and Imbriano,C. (2008) A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response. Nucleic Acids Res., 36 1415-1428.
38. Ceribelli,M., Dolfini,D., Merico,D., Gatta,R., Viganò,A.M., Pavesi,G. and Mantovani,R. (2008) The histone-like NF-Y is a bifunctional transcription factor. Mol. Cell Biol., 28, 2047-2058.
39. Donati,G., Gatta,R., Dolfini,D., Fossati,A., Ceribelli,M. and Mantovani,R. (2008) An NF-Y-dependent switch of positive and negative histone methyl marks on CCAAT promoters. PLoS ONE, 3, e2066.
40. Yuan,G.C., Liu,Y.J., Dion,M.F., Slack,M.D., Wu,L.F., Altschuler,S.J. and Rando,O.J. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science, 309, 626-630.
41. Liu,C.L., Kaplan,T., Kim,M., Buratowski,S., Schreiber,S.L., Friedman,N. and Rando,O.J. (2005) Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol., 3, e328.
42. Ozsolak,F., Song,J.S., Liu,X.S. and Fisher,D.E. (2007) High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol., 25, 244-248.
43. Mavrich,T.N., Jiang,C., Ioshikhes,I.P., Li,X., Venters,B.J., Zanton,S.J., Tomsho,L.P., Qi,J., Glaser,R.L., Schuster,S.C. et al. (2008) Nucleosome organization in the Drosophila genome. Nature 453, 358-362.
44. Schones,D.E., Cui,K., Cuddapah,S., Roh,T.Y., Barski,A., Wang,Z., Wei,G. and Zhao,K. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell, 132, 887-898.
45. Ferrai,C., Munari,D., Luraghi,P., Pecciarini,L., Cangi,M.G., Doglioni,C., Blasi,F. and Crippa,M.P. (2007) A transcription-dependent micrococcal nuclease-resistant fragment of the urokinase-type plasminogen activator promoter interacts with the enhancer. J. Biol. Chem., 282, 12537-12546.
46. Imbriano,C., Gurtner,A., Cocchiarella,F., Di Agostino,S., Basile,V., Gostissa,M., Dobbelstein,M., Del Sal,G., Piaggio,G. and Mantovani,R. (2005) Direct p53 transcriptional repression: in vivo analysis of CCAAT-containing G2/M promoters. Mol. Cell Biol., 25, 3737-3751.
47. Caretti,G., Salsi,V., Vecchi,C., Imbriano,C. and Mantovani,R. (2003) Dynamic recruitment of NF-Y and histone acetyltransferases on cell-cycle promoters. J. Biol. Chem., 278, 30435-30440.
48. Dou,Y., Milne,T.A., Ruthenburg,A.J., Lee,S., Lee,J.W., Verdine,G.L., Allis,C.D. and Roeder,R.G. (2006) Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nat. Struct. Mol. Biol., 13, 71371-71379.
49. Lee,M.G., Wynder,C., Cooch,N. and Shiekhattar,R (2005) An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 437, 432-435.
50. Shi,Y.J., Matson,C., Lan,F., Iwase,S., Baba,T. and Shi,Y. (2005) Regulation of LSD1 histone demethylase activity by its associated factors. Mol. Cell, 19, 857-864.
51. Schotta,G., Lachner,M., Sarma,K., Ebert,A., Sengupta,R., Reuter,G., Reinberg,D. and Jenuwein,T. (2004) A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev. 18, 1251-1262.
52. Mimasu,S., Sengoku,T., Fukuzawa,S., Umehara,T. and Yokoyama,S. (2008) Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A. Biochem. Biophys. Res. Commun., 366, 15-22.
53. Lee,M.G., Wynder,C., Schmidt,D.M., McCafferty,D.G. and Shiekhattar,R. (2006) Histone H3 lysine 4 demethylation is a target of nonselective antidepressive medications. Chem. Biol., 13, 563-567.
54. Tornaletti,S. and Pfeifer,G.P. (1995) UV light as a footprinting agent: modulation of UV-induced DNA damage by transcription factors bound at the promoters of three human genes. J. Mol. Biol., 249, 714-728.
55. Salsi,V., Caretti,G., Wasner,M., Reinhard,W., Haugwitz,U, Engeland,K. and Mantovani,R. (2003) Interactions between p300 and multiple NF-Y trimers govern cyclin B2 promoter function. J. Biol. Chem., 278 6642-6650.
56. Caretti,G., Motta,M.C. and Mantovani,R. (1999) NF-Y associates with H3-H4 tetramers and octamers by multiple mechanisms. Mol. Cell Biol. 19, 8591-8603.
57. Segal,E., Fondufe-Mittendorf,Y., Chen,L., Thastrom,A., Field,Y., Moore,I.K., Wang,J.P. and Widom,J. (2006) A genomic code for nucleosome positioning. Nature, 442, 772-778.
58. Adkins,M.W., Williams,S.K., Linger,J. and Tyler,J.K. (2007) Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators. Mol. Cell Biol. 27, 6372-6382.
59. Williams,S.K. and Tyler,J.K (2007) Transcriptional regulation by chromatin disassembly and reassembly. Curr. Opin. Genet. Dev., 17, 88-93.
60. Kim,J., Hake,S.B. and Roeder,R.G. (2005) The human homolog of yeast BRE1 functions as a transcriptional coactivator through direct activator interactions. Mol. Cell, 20, 759-770.
61. Carrozza,M.J., Li,B., Florens,L., Suganuma,T., Swanson,S.K., Lee,K.K., Shia,W.J., Anderson,S., Yates,J., Washburn,M.P. et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell, 123, 581-592.
62. Joshi,A.A. and Struhl,K. (2005) Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol. Cell, 20, 971-978.
63. Keogh,M.C., Kurdistani,S.K., Morris,S.A., Ahn,S.H., Podolny,V., Collins,S.R., Schuldiner,M., Chin,K., Punna,T., Thompson,N.J. et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell, 123, 593-605.
64. Kizer,K.O., Phatnani,H.P., Shibata,Y., Hall,H., Greenleaf,A.L. and Strahl,B.D. (2005) A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol. Cell Biol., 25, 3305-3316.
65. Kabe,Y., Yamada,J., Uga,H., Yamaguchi,Y., Wada,T. and Handa,H. (2005) NF-Y is essential for the recruitment of RNA polymerase II and inducible transcription of several CCAAT box-containing genes. Mol. Cell Biol. 25, 512-522.
66. Donati,G., Imbriano,C. and Mantovani,R. (2006) Dynamic recruitment of transcription factors and epigenetic changes on the ER stress response gene promoters. Nucleic Acids Res., 34, 3116-3127.
67. Johnson,K.D., Grass,J.A., Park,C., Im,H., Choi,K. and Bresnick,E.H. (2003) Highly restricted localization of RNA polymerase II within a locus control region of a tissue-specific chromatin domain. Mol. Cell Biol., 23, 6484-6493.
68. Masternak,K., Peyraud,N., Krawczyk,M., Barras,E. and Reith,W. (2003) Chromatin remodeling and extragenic transcription at the MHC class II locus control region. Nat. Immunol., 4, 132-137.
69. Scibetta,A.G., Santangelo,S., Coleman,J-, Hall,D-, Chaplin,T., Copier,J., Catchpole,S., Burchell,J. and Taylor-Papadimitriou,J. (2007) Functional analysis of the transcription repressor PLU-1/JARID1B. Mol. Cell Biol., 27, 7220-7235.
70. Tu,S-, Teng,YC., Yuan,C., Wu,Y.T., Chan,M.Y., Cheng,A.N., Lin,P.H., Juan,L.J. and Tsai,M.D. (2008) The ARID domain of the H3K4 demethylase RBP2 binds to a DNA CCGCCC motif. Nat. Struct. Mol. Biol., 15 419-421.
71. Wang,J., Scully,K., Zhu,X., Cai,L., Zhang,J., Prefontaine,G.G., Krones,A., Ohgi,K.A., Zhu,P., Garcia-Bassets,I. et al. (2007) Opposing LSD1 complexes function in developmental gene activation and repression programmes. Nature, 446, 882-887.
72. Saleque,S., Kim,J., Rooke,H.M. and Orkin,S.H. (2007) Epigenetic regulation of hematopoietic differentiation by G.-1 and G.-1b is mediated by the cofactors CoREST and LSD1. Mol. Cell, 27, 562-572.
73. You,A., Tong,J.K., Grozinger,C.M. and Schreiber,S.L. (2001) CoREST is an integral component of the CoREST-human histone deacetylase complex. Proc. Natl Acad. Sci. USA, 98, 1454-1458.
74. Yamagoe,S., Kanno,T., Kanno,Y., Sasaki,S., Siegel,R.M., Lenardo,M.J., Humphrey,G., Wang,Y., Nakatani,Y., Howard,B.H. et al. (2003) Interaction of histone acetylases and deacetylases in vivo. Mol. Cell Biol., 23, 1025-1033.
75. Wissmann,M., Yin,N., Müller,J.M., Greschik,H., Fodor,B.D., Jenuwein,T., Vogler,C., Schneider,R., Günther,T., Buettner,R. et al. (2007) Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat. Cell Biol., 9 347-353.
76. Metzger,E., Wissmann,M., Yin,N., Müller,J.M., Schneider,R., Peters,A.H., Günther,T., Buettner,R. and Schüle,R. (2005) LSD1 demethylates repressive histone marks to promote androgen-receptor- dependent transcription. Nature, 437, 436-439.
77. Perillo,B., Ombra,M.N., Bertoni,A., Cuozzo,C., Sacchetti,S., Sasso,A., Chiariotti,L., Malorni,A., Abbondanza,C. and Avvedimento,E.V. (2008) DNA oxidation as triggered by H3K9me2 demethylation drives estrogen-induced gene expression. Science, 319, 202-206.
78. Garcia-Bassets,I., Kwon,Y.S., Telese,F., Prefontaine,G.G., Hutt,K.R., Cheng,C.S., Ju,B.G., Ohgi,K.A., Wang,J., Escoubet-Lozach,L. et al. (2007) Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell, 128, 505-518.
79. Chau,C.M., Deng,Z., Kang,H. and Lieberman,P.M. (2008) Cell cycle association of the retinoblastoma protein Rb and the histone demethylase LSD1 with the Epstein-Barr virus latency promoter Cp. J. Virol., 82, 3428-3437.
80. Yang,M., Gocke,C.B., Luo,X., Borek,D., Tomchick,D.R., Machius,M., Otwinowski,Z. and Yu,H. (2006) Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. Mol. Cell, 23, 377-387.
81. Hakimi,M.A., Dong,Y., Lane,W.S., Speicher,D.W. and Shiekhattar,R. (2003) A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. J. Biol. Chem. 278, 7234-7239.
82. Shi,Y., Sawada,J., Sui,G., Affar el,B., Whetstine,J.R., Lan,F., Ogawa,H., Luke,M.P., Nakatani,Y. and Shi,Y. (2003) Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature, 422, 735-738.
83. Cowger,J.J., Zhao,Q., Isovic,M. and Torchia,J. (2006) Biochemical characterization of the zinc-finger protein 217 transcriptional repressor complex: Identification of a ZNF217 consensus recognition sequence. Oncogene, 26, 3378-3386.