Home LiteratureArticle Details
该文献已被撤稿（Retracted Publication），引用前请核实。
PMID: 16735507 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Retracted Publication

Role of DNA methyltransferases in regulation of human ribosomal RNA gene transcription.

The Journal of biological chemistry ·Vol. 281 ·No. 31 ·2006-08-04 ·Pages 22062-22072a

Majumder S, Ghoshal K, Datta J, Smith DS, Bai S, Jacob ST

Abstract

We have previously demonstrated that the expression of human ribosomal RNA genes (rDNA) in normal and cancer cells is differentially regulated by methylation of the promoter CpG islands. Furthermore, we showed that the methyl CpG-binding protein MBD2 plays a selective role in the methylation-mediated block in rDNA expression. Here, we analyzed the role of three functional mammalian DNA methyltransferases (DNMTs) in regulating the rDNA promoters activity. Immunofluorescence analysis and biochemical fractionation showed that all three DNMTs (DNMT1, DNMT3A, and DNMT3B) are associated with the inactive rDNA in the nucleolus. Although DNMTs associate with both methylated and unmethylated rDNA promoters, DNMT1 preferentially associates with the methylated genes. The rDNA primary transcript level was significantly elevated in DNMT1-/- or DNMT3B-/- human colon carcinoma (HCT116) cells. Southern blot analysis demonstrated a moderate level of rDNA promoter hypomethylation in DNMT1-/- cells and a dramatic loss of rDNA promoter methylation in double knockout cells. Transient overexpression of DNMT1 or DNMT3B suppressed the luciferase expression from both methylated and unmethylated pHrD-IRES-Luc, a reporter plasmid where the rDNA promoter drives luciferase expression. DNMT1-mediated suppression of the unmethylated promoter involves de novo methylation of the promoter, whereas histone deacetylase 2 cooperates with DNMT1 to inhibit the methylated rDNA promoter. Unlike DNMT1, both the wild type and catalytically inactive DNMT3B mutant can suppress rDNA promoter irrespective of its methylation status. DNMT3B-mediated suppression of the rDNA promoter also involves histone deacetylation. Treatment of HCT116 cells with Decitabine (a DNMT inhibitor) or trichostatin A (a histone deacetylase inhibitor) up-regulated endogenous rDNA expression. These inhibitors synergistically activated methylated pHrD-IRES-Luc, whereas they exhibited additive effects on the unmethylated promoter. These results demonstrate localization of DNMTs with the inactive rDNA in the nucleolus, the specific role of DNMT1 and DNMT3B in rDNA expression and the differential regulation of rDNA expression from the methylated and unmethylated rDNA promoters.

MeSH Terms
Animals Cell Line DNA (Cytosine-5-)-Methyltransferase 1 DNA (Cytosine-5-)-Methyltransferases/physiology DNA Methylation DNA Methyltransferase 3A DNA Modification Methylases/physiology DNA, Ribosomal/genetics Gene Expression Regulation Humans Mice Promoter Regions, Genetic RNA, Ribosomal/genetics Transcription, Genetic Transfection
Chemicals
DNA, Ribosomal DNMT3A protein, human Dnmt3a protein, mouse RNA, Ribosomal DNA Modification Methylases DNA (Cytosine-5-)-Methyltransferase 1 DNA (Cytosine-5-)-Methyltransferases DNA Methyltransferase 3A DNA methyltransferase 3B DNMT1 protein, human Dnmt1 protein, mouse
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Majumder Sarmila
Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210. Electronic address: majumder.2@osu.edu.
Ghoshal Kalpana
Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210.
Datta Jharna
Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210.
Smith David Spencer
Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210.
Bai Shoumei
Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210.
Jacob Samson T
Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210. Electronic address: jacob.42@osu.edu.
References (54)
54 references, click to expand
  1. The DNA methyltransferases of mammals.
    Hum Mol Genet. 2000 Oct;9(16):2395-402 PMID: 11005794
  2. The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription.
    Nat Genet. 2002 Nov;32(3):393-6 PMID: 12368916
  3. Histone methylation versus histone acetylation: new insights into epigenetic regulation.
    Curr Opin Cell Biol. 2001 Jun;13(3):263-73 PMID: 11343896
  4. Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription.
    EMBO J. 2001 May 15;20(10):2536-44 PMID: 11350943
  5. Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin.
    J Biol Chem. 2001 Aug 24;276(34):32282-7 PMID: 11427539
  6. Use of chromatin immunoprecipitation to clone novel E2F target promoters.
    Mol Cell Biol. 2001 Oct;21(20):6820-32 PMID: 11564866
  7. Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription.
    Mol Cell. 2001 Sep;8(3):719-25 PMID: 11583633
  8. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development.
    Cell. 1999 Oct 29;99(3):247-57 PMID: 10555141
  9. Methylation-induced repression--belts, braces, and chromatin.
    Cell. 1999 Nov 24;99(5):451-4 PMID: 10589672
  10. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci.
    Nat Genet. 2000 Jul;25(3):269-77 PMID: 10888872
  11. DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters.
    Nat Genet. 2000 Jul;25(3):338-42 PMID: 10888886
  12. Inhibitors of histone deacetylase and DNA methyltransferase synergistically activate the methylated metallothionein I promoter by activating the transcription factor MTF-1 and forming an open chromatin structure.
    Mol Cell Biol. 2002 Dec;22(23):8302-19 PMID: 12417732
  13. Oddpols united: new insights into transcription by RNA polymerases I and III.
    Gene Expr. 2002;10(5-6):263-9 PMID: 12450218
  14. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals.
    Nat Genet. 2003 Mar;33 Suppl:245-54 PMID: 12610534
  15. Biochemical fractionation reveals association of DNA methyltransferase (Dnmt) 3b with Dnmt1 and that of Dnmt 3a with a histone H3 methyltransferase and Hdac1.
    J Cell Biochem. 2003 Apr 1;88(5):855-64 PMID: 12616525
  16. Epigenetic silencing of RNA polymerase I transcription.
    Nat Rev Mol Cell Biol. 2003 Aug;4(8):641-9 PMID: 12923526
  17. Decitabine.
    Curr Opin Oncol. 2003 Nov;15(6):446-51 PMID: 14624227
  18. Role of human ribosomal RNA (rRNA) promoter methylation and of methyl-CpG-binding protein MBD2 in the suppression of rRNA gene expression.
    J Biol Chem. 2004 Feb 20;279(8):6783-93 PMID: 14610093
  19. A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance.
    Mol Cell. 2004 Feb 27;13(4):599-609 PMID: 14992728
  20. Structure and function of eukaryotic DNA methyltransferases.
    Curr Top Dev Biol. 2004;60:55-89 PMID: 15094296
  21. DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system.
    Biochem Biophys Res Commun. 2004 May 28;318(2):544-55 PMID: 15120635
  22. Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery.
    Nucleic Acids Res. 2004;32(9):2716-29 PMID: 15148359
  23. Reversal of gene silencing as a therapeutic target for cancer--roles for DNA methylation and its interdigitation with chromatin.
    Novartis Found Symp. 2004;259:226-33; discussion 234-7, 285-8 PMID: 15171257
  24. The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin.
    Mol Cell Biol. 2004 Oct;24(20):9048-58 PMID: 15456878
  25. Repeated genes in eukaryotes.
    Annu Rev Biochem. 1980;49:727-64 PMID: 6996571
  26. Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle.
    Cell. 1989 Jun 2;57(5):753-61 PMID: 2720786
  27. Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain.
    EMBO J. 1992 Jul;11(7):2611-7 PMID: 1628623
  28. A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei.
    Cell. 1992 Nov 27;71(5):865-73 PMID: 1423634
  29. DNA methyltransferases.
    Curr Opin Cell Biol. 1994 Jun;6(3):380-9 PMID: 7917329
  30. CpG islands and genes.
    Curr Opin Genet Dev. 1995 Jun;5(3):309-14 PMID: 7549424
  31. Characterisation of independent DNA and multiple Zn-binding domains at the N terminus of human DNA-(cytosine-5) methyltransferase: modulating the property of a DNA-binding domain by contiguous Zn-binding motifs.
    J Mol Biol. 1996 Apr 19;257(5):935-48 PMID: 8632476
  32. Histones associated with non-nucleosomal rat ribosomal genes are acetylated while those bound to nucleosome-organized gene copies are not.
    J Biol Chem. 1996 May 17;271(20):11852-7 PMID: 8662629
  33. Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1.
    Science. 1997 Sep 26;277(5334):1996-2000 PMID: 9302295
  34. Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer.
    Nat Genet. 1999 Jan;21(1):103-7 PMID: 9916800
  35. Biochemistry and biology of mammalian DNA methyltransferases.
    Cell Mol Life Sci. 2004 Oct;61(19-20):2571-87 PMID: 15526163
  36. ISOLATION OF NUCLEOLI.
    Exp Cell Res. 1963;24:SUPPL9:150-63 PMID: 14046224
  37. DNA methyltransferase 3b regulates nerve growth factor-induced differentiation of PC12 cells by recruiting histone deacetylase 2.
    Mol Cell Biol. 2005 Jan;25(2):751-66 PMID: 15632075
  38. Epigenetic mechanism of rRNA gene silencing: temporal order of NoRC-mediated histone modification, chromatin remodeling, and DNA methylation.
    Mol Cell Biol. 2005 Apr;25(7):2539-46 PMID: 15767661
  39. Epigenetic reprogramming in mammals.
    Hum Mol Genet. 2005 Apr 15;14 Spec No 1:R47-58 PMID: 15809273
  40. Eukaryotic cytosine methyltransferases.
    Annu Rev Biochem. 2005;74:481-514 PMID: 15952895
  41. DNA methylation and histone modifications: teaming up to silence genes.
    Curr Opin Genet Dev. 2005 Oct;15(5):490-5 PMID: 16098738
  42. Physical and functional interaction of DNA methyltransferase 3A with Mbd3 and Brg1 in mouse lymphosarcoma cells.
    Cancer Res. 2005 Dec 1;65(23):10891-900 PMID: 16322236
  43. De novo CpG island methylation in human cancer cells.
    Cancer Res. 2006 Jan 15;66(2):682-92 PMID: 16423997
  44. 5-Aza-deoxycytidine induces selective degradation of DNA methyltransferase 1 by a proteasomal pathway that requires the KEN box, bromo-adjacent homology domain, and nuclear localization signal.
    Mol Cell Biol. 2005 Jun;25(11):4727-41 PMID: 15899874
  45. The role of acetylation in rDNA transcription.
    Nucleic Acids Res. 2001 Oct 15;29(20):4114-24 PMID: 11600700
  46. Regulation of ribosome biogenesis within the nucleolus.
    FEBS Lett. 2001 Dec 7;509(2):145-50 PMID: 11741579
  47. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.
    Nat Struct Biol. 2002 Mar;9(3):217-24 PMID: 11836534
  48. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases.
    Chembiochem. 2002 Apr 2;3(4):274-93 PMID: 11933228
  49. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells.
    Nature. 2002 Apr 4;416(6880):552-6 PMID: 11932749
  50. Role of de novo DNA methyltransferases and methyl CpG-binding proteins in gene silencing in a rat hepatoma.
    J Biol Chem. 2002 May 3;277(18):16048-58 PMID: 11844796
  51. DNA methylation and chromatin - unraveling the tangled web.
    Oncogene. 2002 Aug 12;21(35):5361-79 PMID: 12154399
  52. 5-Azacytidine and 5-aza-2'-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy.
    Oncogene. 2002 Aug 12;21(35):5483-95 PMID: 12154409
  53. Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together?
    J Cell Biochem. 2002;87(2):117-25 PMID: 12244565
  54. DNA methylation and histone deacetylation in the control of gene expression: basic biochemistry to human development and disease.
    Gene Expr. 2000;9(1-2):63-75 PMID: 11097425
Article Info
Journal
The Journal of biological chemistry
Abbr.
J Biol Chem
ISSN
0021-9258
DOI
10.1074/jbc.M601155200
Email
majumder.2@osu.edu
jacob.42@osu.edu
Published
2006-08-04
Epub
2006-00-30
Pages
22062-22072a
Language
English
Region
United States
NLM ID
2985121R
PMCID
PMC2243234
Subset
IM
Grants
NCI NIH HHS · R01 CA086978 · United States
NCI NIH HHS · R01 CA086978-01A2 · United States
NIEHS NIH HHS · ES10874 · United States
NIEHS NIH HHS · R01 ES010874-02 · United States
NCI NIH HHS · R01 CA086978-05 · United States
NCI NIH HHS · R01 CA086978-06A1 · United States
NCI NIH HHS · R01 CA086978-04 · United States
NIEHS NIH HHS · R01 ES010874-01 · United States
NIEHS NIH HHS · R01 ES010874 · United States
NIEHS NIH HHS · R01 ES010874-05 · United States
NCI NIH HHS · CA86978 · United States
NCI NIH HHS · R01 CA086978-02 · United States
NCI NIH HHS · R01 CA086978-03 · United States
NIEHS NIH HHS · R01 ES010874-04 · United States
NIEHS NIH HHS · R01 ES010874-03 · United States
Corrections
RetractionIn
PMID: 29523697
External Links
PubMed source DOI: 10.1074/jbc.M601155200 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2