Epigenetic mechanism of rRNA gene silencing: temporal order of NoRC-mediated histone modification, chromatin remodeling, and DNA methylation.

PubWeight™: 1.66‹?› | Rank: Top 3%

🔗 View Article (PMC 1061655)

Published in Mol Cell Biol on April 01, 2005

Authors

Raffaella Santoro1, Ingrid Grummt

Author Affiliations

1: German Cancer Research Center, Division of Molecular Biology of the Cell II, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. r.santoro@dkfz-heidelberg.de

Articles citing this

Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol Cell (2008) 1.94

PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Nat Struct Mol Biol (2010) 1.91

The structure of NoRC-associated RNA is crucial for targeting the chromatin remodelling complex NoRC to the nucleolus. EMBO Rep (2008) 1.64

UBF levels determine the number of active ribosomal RNA genes in mammals. J Cell Biol (2008) 1.57

The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats. EMBO J (2010) 1.40

NoRC-dependent nucleosome positioning silences rRNA genes. EMBO J (2006) 1.39

Modeling the dynamics of transcriptional gene regulatory networks for animal development. Dev Biol (2008) 1.37

Transcription regulation of the rRNA gene by a multifunctional nucleolar protein, B23/nucleophosmin, through its histone chaperone activity. Mol Cell Biol (2008) 1.30

Nucleolar dominance and ribosomal RNA gene silencing. Curr Opin Cell Biol (2010) 1.19

The nucleolus—guardian of cellular homeostasis and genome integrity. Chromosoma (2013) 1.14

Chromatin: linking structure and function in the nucleolus. Chromosoma (2008) 1.14

Potential of DNMT and its Epigenetic Regulation for Lung Cancer Therapy. Curr Genomics (2009) 1.11

Nucleosomes protect DNA from DNA methylation in vivo and in vitro. Nucleic Acids Res (2011) 1.08

Role of DNA methyltransferases in regulation of human ribosomal RNA gene transcription. J Biol Chem (2006) 1.06

Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans. EMBO Rep (2009) 1.05

CAG expansion induces nucleolar stress in polyglutamine diseases. Proc Natl Acad Sci U S A (2012) 1.05

Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription. Nucleic Acids Res (2012) 1.05

Actin complexes in the cell nucleus: new stones in an old field. Histochem Cell Biol (2010) 1.04

Allelic inactivation of rDNA loci. Genes Dev (2009) 1.04

Methylation of histone H3 and H4 by PRMT5 regulates ribosomal RNA gene transcription. J Cell Biochem (2010) 1.01

Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation. J Mol Cell Biol (2014) 1.00

Structure and function of ribosomal RNA gene chromatin. Biochem Soc Trans (2008) 0.98

Epigenetic programming of the rRNA promoter by MBD3. Mol Cell Biol (2007) 0.95

Global heterochromatin loss: a unifying theory of aging? Epigenetics (2012) 0.95

The Roles of the Methyl-CpG Binding Proteins in Cancer. Genes Cancer (2011) 0.94

SAP30L interacts with members of the Sin3A corepressor complex and targets Sin3A to the nucleolus. Nucleic Acids Res (2006) 0.94

Basic mechanisms in RNA polymerase I transcription of the ribosomal RNA genes. Subcell Biochem (2013) 0.94

Structure and epigenetics of nucleoli in comparison with non-nucleolar compartments. J Histochem Cytochem (2009) 0.93

ATP dependent chromatin remodeling enzymes in embryonic stem cells. Stem Cell Rev (2010) 0.92

The N-CoR complex enables chromatin remodeler SNF2H to enhance repression by thyroid hormone receptor. EMBO J (2006) 0.91

Histones are required for transcription of yeast rRNA genes by RNA polymerase I. Proc Natl Acad Sci U S A (2005) 0.90

CpG methylation in neurons: message, memory, or mask? Neuropsychopharmacology (2010) 0.89

An intranucleolar body associated with rDNA. Chromosoma (2011) 0.89

The chromatin remodelling complex B-WICH changes the chromatin structure and recruits histone acetyl-transferases to active rRNA genes. PLoS One (2011) 0.89

SUV39h-independent association of HP1 beta with fibrillarin-positive nucleolar regions. Chromosoma (2009) 0.89

A RUNX2-HDAC1 co-repressor complex regulates rRNA gene expression by modulating UBF acetylation. J Cell Sci (2012) 0.88

Identification and characterization of ToRC, a novel ISWI-containing ATP-dependent chromatin assembly complex. Genes Dev (2012) 0.84

Functional ultrastructure of the plant nucleolus. Protoplasma (2014) 0.82

Epigeneitc silencing of ribosomal RNA genes by Mybbp1a. J Biomed Sci (2012) 0.82

Angiogenin stimulates ribosomal RNA transcription by epigenetic activation of the ribosomal DNA promoter. J Cell Physiol (2014) 0.82

Chromatin structure of ribosomal genes in Chironomus thummi (Diptera: Chironomidae): tissue specificity and behaviour under drug treatment. Chromosome Res (2007) 0.81

Epigenetic engineering of ribosomal RNA genes enhances protein production. PLoS One (2009) 0.81

Identification of imprinting regulators at the Meg3 differentially methylated region. Genomics (2012) 0.80

Ribosomal protein S6, a target of rapamycin, is involved in the regulation of rRNA genes by possible epigenetic changes in Arabidopsis. J Biol Chem (2013) 0.79

Sex-specific methylation in Drosophila: an investigation of the Sophophora subgenus. Genetica (2010) 0.78

Characterization of Dnmt1 Binding and DNA Methylation on Nucleosomes and Nucleosomal Arrays. PLoS One (2015) 0.76

Overexpression of Ribosomal RNA in the Development of Human Cervical Cancer Is Associated with rDNA Promoter Hypomethylation. PLoS One (2016) 0.75

Analysis of histone modifications at human ribosomal DNA in liver cancer cell. Sci Rep (2015) 0.75

The Epigenetic Pathways to Ribosomal DNA Silencing. Microbiol Mol Biol Rev (2016) 0.75

ING1 regulates rRNA levels by altering nucleolar chromatin structure and mTOR localization. Nucleic Acids Res (2016) 0.75

Nucleolar Reorganization Upon Site-Specific Double-Strand Break Induction: DNA Repair and Epigenetics of Ribosomal Genes. J Histochem Cytochem (2016) 0.75

The Nucleolus: In Genome Maintenance and Repair. Int J Mol Sci (2017) 0.75

A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription. PLoS Genet (2017) 0.75

Articles cited by this

Translating the histone code. Science (2001) 56.77

The language of covalent histone modifications. Nature (2000) 44.92

Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature (1998) 18.36

Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet (1998) 13.27

Repeated genes in eukaryotes. Annu Rev Biochem (1980) 11.23

A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature (2001) 8.27

Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. Cell (2000) 6.32

Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell (2002) 6.25

Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat Genet (2002) 5.86

DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nat Genet (2000) 5.72

DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nat Genet (2000) 5.29

Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol (2002) 4.98

Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science (2002) 4.49

The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res (2003) 4.36

ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev (1999) 3.85

The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo. Mol Cell (2000) 3.62

The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nat Genet (2002) 3.58

Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell (1989) 3.51

Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev (2001) 2.96

The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell (2000) 2.95

A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell (2004) 2.92

Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol Cell Biol (2001) 2.67

NoRC--a novel member of mammalian ISWI-containing chromatin remodeling machines. EMBO J (2001) 2.67

Modulation of ISWI function by site-specific histone acetylation. EMBO Rep (2002) 2.54

The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev (1998) 2.41

The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription. EMBO J (2002) 2.36

WSTF-ISWI chromatin remodeling complex targets heterochromatic replication foci. EMBO J (2002) 2.33

A family of chromatin remodeling factors related to Williams syndrome transcription factor. Proc Natl Acad Sci U S A (2000) 2.24

Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription. Mol Cell (2001) 2.24

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 (2003) 2.15

Purification and characterization of a human factor that assembles and remodels chromatin. J Biol Chem (2000) 2.13

HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. EMBO J (2000) 2.11

ATP-driven chromatin remodeling activity and histone acetyltransferases act sequentially during transactivation by RAR/RXR In vitro. Mol Cell (2000) 1.83

Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression. J Biol Chem (2003) 1.71

A transient histone hyperacetylation signal marks nucleosomes for remodeling at the PHO8 promoter in vivo. Mol Cell (2001) 1.70

Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together? J Cell Biochem (2002) 1.67

Trichostatin A causes selective loss of DNA methylation in Neurospora. Proc Natl Acad Sci U S A (1998) 1.66

ATP-dependent chromatin remodeling factors: nucleosome shufflers with many missions. Oncogene (2001) 1.59

Lsh, a modulator of CpG methylation, is crucial for normal histone methylation. EMBO J (2003) 1.40

The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo. Nucleic Acids Res (2004) 1.16

Recruitment of the nucleolar remodeling complex NoRC establishes ribosomal DNA silencing in chromatin. Mol Cell Biol (2004) 1.15

Histones associated with non-nucleosomal rat ribosomal genes are acetylated while those bound to nucleosome-organized gene copies are not. J Biol Chem (1996) 1.11

Lashings of DNA methylation, forkfuls of chromatin remodeling. Genes Dev (2001) 1.00

Articles by these authors

A kinetic framework for a mammalian RNA polymerase in vivo. Science (2002) 4.42

c-Myc associates with ribosomal DNA and activates RNA polymerase I transcription. Nat Cell Biol (2005) 3.79

The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nat Genet (2002) 3.58

The epigenetics of rRNA genes: from molecular to chromosome biology. Annu Rev Cell Dev Biol (2008) 3.42

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev (2010) 2.96

mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes Dev (2004) 2.96

Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol Cell (2006) 2.89

Nuclear actin and myosin I are required for RNA polymerase I transcription. Nat Cell Biol (2004) 2.49

Mammalian Sir2 homolog SIRT7 is an activator of RNA polymerase I transcription. Genes Dev (2006) 2.47

Genetic inactivation of the transcription factor TIF-IA leads to nucleolar disruption, cell cycle arrest, and p53-mediated apoptosis. Mol Cell (2005) 2.46

The RNA polymerase I transcription machinery: an emerging target for the treatment of cancer. Annu Rev Pharmacol Toxicol (2010) 2.45

The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription. EMBO J (2002) 2.36

The nucleolus as a stress sensor: JNK2 inactivates the transcription factor TIF-IA and down-regulates rRNA synthesis. Genes Dev (2005) 2.13

ERK-dependent phosphorylation of the transcription initiation factor TIF-IA is required for RNA polymerase I transcription and cell growth. Mol Cell (2003) 1.98

TAF12 recruits Gadd45a and the nucleotide excision repair complex to the promoter of rRNA genes leading to active DNA demethylation. Mol Cell (2009) 1.97

Activation of RNA polymerase I transcription by cockayne syndrome group B protein and histone methyltransferase G9a. Mol Cell (2007) 1.96

CSB is a component of RNA pol I transcription. Mol Cell (2002) 1.93

PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Nat Struct Mol Biol (2010) 1.91

Cellular stress and nucleolar function. Cell Cycle (2005) 1.88

Identification of novel functional TBP-binding sites and general factor repertoires. EMBO J (2007) 1.77

The PHD finger/bromodomain of NoRC interacts with acetylated histone H4K16 and is sufficient for rDNA silencing. Curr Biol (2005) 1.75

The structure of NoRC-associated RNA is crucial for targeting the chromatin remodelling complex NoRC to the nucleolus. EMBO Rep (2008) 1.64

Nuclear myosin I acts in concert with polymeric actin to drive RNA polymerase I transcription. Genes Dev (2008) 1.63

The chromatin remodelling complex WSTF-SNF2h interacts with nuclear myosin 1 and has a role in RNA polymerase I transcription. EMBO Rep (2006) 1.59

The chromatin remodelling complex NoRC safeguards genome stability by heterochromatin formation at telomeres and centromeres. EMBO Rep (2013) 1.55

Multiple interactions between RNA polymerase I, TIF-IA and TAF(I) subunits regulate preinitiation complex assembly at the ribosomal gene promoter. EMBO Rep (2002) 1.48

Modulation of RNA polymerase assembly dynamics in transcriptional regulation. Mol Cell (2008) 1.47

TFIIH plays an essential role in RNA polymerase I transcription. Cell (2002) 1.43

Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells. Nucleic Acids Res (2007) 1.42

Repression of RNA polymerase I upon stress is caused by inhibition of RNA-dependent deacetylation of PAF53 by SIRT7. Mol Cell (2013) 1.41

The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats. EMBO J (2010) 1.40

AMP-activated protein kinase adapts rRNA synthesis to cellular energy supply. Proc Natl Acad Sci U S A (2009) 1.40

NoRC-dependent nucleosome positioning silences rRNA genes. EMBO J (2006) 1.39

NuRD blocks reprogramming of mouse somatic cells into pluripotent stem cells. Stem Cells (2013) 1.35

The chromatin remodeling complex NoRC controls replication timing of rRNA genes. EMBO J (2004) 1.34

Reversible acetylation of the chromatin remodelling complex NoRC is required for non-coding RNA-dependent silencing. Nat Cell Biol (2009) 1.30

Nucleolar disruption in dopaminergic neurons leads to oxidative damage and parkinsonism through repression of mammalian target of rapamycin signaling. J Neurosci (2011) 1.20

The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo. Nucleic Acids Res (2004) 1.16

Recruitment of the nucleolar remodeling complex NoRC establishes ribosomal DNA silencing in chromatin. Mol Cell Biol (2004) 1.15

The nucleolus—guardian of cellular homeostasis and genome integrity. Chromosoma (2013) 1.14

The chromatin remodeling complex NuRD establishes the poised state of rRNA genes characterized by bivalent histone modifications and altered nucleosome positions. Proc Natl Acad Sci U S A (2012) 1.13

Activation of an endogenous suicide response after perturbation of rRNA synthesis leads to neurodegeneration in mice. J Neurosci (2008) 1.12

Phosphorylation by casein kinase 2 facilitates rRNA gene transcription by promoting dissociation of TIF-IA from elongating RNA polymerase I. Mol Cell Biol (2008) 1.10

Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans. EMBO Rep (2009) 1.05

Human Cdc14B promotes progression through mitosis by dephosphorylating Cdc25 and regulating Cdk1/cyclin B activity. PLoS One (2011) 1.01

Acetylation of UBF changes during the cell cycle and regulates the interaction of UBF with RNA polymerase I. Nucleic Acids Res (2006) 0.94

Proteasomal ATPases are associated with rDNA: the ubiquitin proteasome system plays a direct role in RNA polymerase I transcription. Biochim Biophys Acta (2008) 0.94

A model for the topology of active ribosomal RNA genes. EMBO Rep (2011) 0.93

Role of pescadillo and upstream binding factor in the proliferation and differentiation of murine myeloid cells. Mol Cell Biol (2004) 0.91

Linking rDNA transcription to the cellular energy supply. Cell Cycle (2010) 0.90

Identification of protein phosphorylation sites by combination of elastase digestion, immobilized metal affinity chromatography, and quadrupole-time of flight tandem mass spectrometry. Proteomics (2002) 0.88

Development of a species-specific RNA polymerase I-based shRNA expression vector. Nucleic Acids Res (2006) 0.86

Death-effector domain-containing protein DEDD is an inhibitor of mitotic Cdk1/cyclin B1. Proc Natl Acad Sci U S A (2007) 0.84

DNA sequence encoded repression of rRNA gene transcription in chromatin. Nucleic Acids Res (2010) 0.84

Dynamic subcellular partitioning of the nucleolar transcription factor TIF-IA under ribotoxic stress. Biochim Biophys Acta (2009) 0.80

Chromatin-specific regulation of mammalian rDNA transcription by clustered TTF-I binding sites. PLoS Genet (2013) 0.79

Mechanism of inhibition of RNA polymerase I transcription by DNA-dependent protein kinase. Biol Chem (2002) 0.79

Autoantibodies to NOR 90/hUBF: longterm clinical and serological followup in a patient with limited systemic sclerosis suggests an antigen driven immune response. J Rheumatol (2002) 0.75