Published in G3 (Bethesda) on February 19, 2014
Nucleolar DNA: the host and the guests. Histochem Cell Biol (2016) 0.95
Conditional inactivation of Upstream Binding Factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body. PLoS Genet (2014) 0.85
Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders. Genome Biol (2016) 0.80
The Regulation of rRNA Gene Transcription during Directed Differentiation of Human Embryonic Stem Cells. PLoS One (2016) 0.78
Nucleolar organizer regions: genomic 'dark matter' requiring illumination. Genes Dev (2016) 0.77
SHPRH regulates rRNA transcription by recognizing the histone code in an mTOR-dependent manner. Proc Natl Acad Sci U S A (2017) 0.75
Serum starvation-induced cell cycle synchronization stimulated mouse rDNA transcription reactivation during somatic cell reprogramming into iPSCs. Stem Cell Res Ther (2016) 0.75
Folate deficiency facilitates recruitment of upstream binding factor to hot spots of DNA double-strand breaks of rRNA genes and promotes its transcription. Nucleic Acids Res (2016) 0.75
The Epigenetic Pathways to Ribosomal DNA Silencing. Microbiol Mol Biol Rev (2016) 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
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science (2002) 24.31
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet (2006) 20.76
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
A unique chromatin signature uncovers early developmental enhancers in humans. Nature (2010) 14.02
New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature (2007) 13.54
Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell (2002) 13.05
Derivation of pluripotent epiblast stem cells from mammalian embryos. Nature (2007) 11.72
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Regulation of chromatin by histone modifications. Cell Res (2011) 8.44
Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Nature (2008) 8.38
Does the ribosome translate cancer? Nat Rev Cancer (2003) 6.89
Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics (2005) 5.08
Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol (2006) 5.01
An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell (2010) 5.00
c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I. Nat Cell Biol (2005) 4.89
The post-transcriptional steps of eukaryotic ribosome biogenesis. Cell Mol Life Sci (2008) 4.87
F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (2008) 4.77
ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods (2009) 4.69
An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc Natl Acad Sci U S A (2009) 4.07
c-Myc associates with ribosomal DNA and activates RNA polymerase I transcription. Nat Cell Biol (2005) 3.79
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 3.57
The epigenetics of rRNA genes: from molecular to chromosome biology. Annu Rev Cell Dev Biol (2008) 3.42
CHD7 cooperates with PBAF to control multipotent neural crest formation. Nature (2010) 2.88
Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia. Cell (2001) 2.86
Structure and function of the nucleolus. Curr Opin Cell Biol (1999) 2.81
Ribosomal protein S19 deficiency in zebrafish leads to developmental abnormalities and defective erythropoiesis through activation of p53 protein family. Blood (2008) 2.68
The nucleolus: an organelle formed by the act of building a ribosome. Curr Opin Cell Biol (1995) 2.59
Ribosomal protein L24 defect in belly spot and tail (Bst), a mouse Minute. Development (2004) 2.54
The transcriptional and signalling networks of pluripotency. Nat Cell Biol (2011) 2.54
A Drosophila Minute gene encodes a ribosomal protein. Nature (1985) 2.53
Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome. Nat Genet (2010) 2.52
Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res (2011) 2.48
Tbx3 improves the germ-line competency of induced pluripotent stem cells. Nature (2010) 2.46
Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science (2005) 2.36
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A (2013) 2.33
Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Cell Stem Cell (2009) 2.32
A RUNX2/PEBP2alpha A/CBFA1 mutation displaying impaired transactivation and Smad interaction in cleidocranial dysplasia. Proc Natl Acad Sci U S A (2000) 2.31
Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res (2009) 2.31
The correlation between rDNA copy number and genome size in eukaryotes. Genome (2003) 2.26
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet (2010) 2.20
Regulation of mammalian ribosomal gene transcription by RNA polymerase I. Prog Nucleic Acid Res Mol Biol (1999) 2.20
RNA-polymerase-I-directed rDNA transcription, life and works. Trends Biochem Sci (2005) 2.13
A Drosophila rRNA gene located in euchromatin is active in transcription and nucleolus formation. Genes Dev (1988) 2.01
A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis. Cell Mol Life Sci (2007) 1.98
PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells. Cell Stem Cell (2013) 1.96
Treacher Collins syndrome: etiology, pathogenesis and prevention. Eur J Hum Genet (2008) 1.64
MAD1 and c-MYC regulate UBF and rDNA transcription during granulocyte differentiation. EMBO J (2004) 1.64
Competitive recruitment of CBP and Rb-HDAC regulates UBF acetylation and ribosomal transcription. Mol Cell (2000) 1.47
Loss of ribosomal protein L11 affects zebrafish embryonic development through a p53-dependent apoptotic response. PLoS One (2009) 1.36
Perturbation of rRNA synthesis in the bap28 mutation leads to apoptosis mediated by p53 in the zebrafish central nervous system. J Biol Chem (2006) 1.36
Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. EMBO J (2013) 1.35
Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacer. Genomics (1995) 1.34
Mi-2 beta associates with BRG1 and RET finger protein at the distinct regions with transcriptional activating and repressing abilities. J Biol Chem (2003) 1.26
Loss of human ribosomal gene CpG methylation enhances cryptic RNA polymerase II transcription and disrupts ribosomal RNA processing. Mol Cell (2009) 1.25
Ribosomal protein gene knockdown causes developmental defects in zebrafish. PLoS One (2006) 1.24
Differential regulation of E2F1, DP1, and the E2F1/DP1 complex by ARF. Mol Cell Biol (2002) 1.23
Phenotypic transcription factors epigenetically mediate cell growth control. Proc Natl Acad Sci U S A (2008) 1.21
Microspherule protein 1, Mi-2beta, and RET finger protein associate in the nucleolus and up-regulate ribosomal gene transcription. J Biol Chem (2005) 1.20
Integrative genomic analysis of human ribosomal DNA. Nucleic Acids Res (2011) 1.18
Complete sequence of the 45-kb mouse ribosomal DNA repeat: analysis of the intergenic spacer. Genomics (2003) 1.14
CHD7 functions in the nucleolus as a positive regulator of ribosomal RNA biogenesis. Hum Mol Genet (2010) 1.13
The nucleolus: reviewing oldies to have new understandings. Cell Res (2006) 1.04
Noncoding transcripts in sense and antisense orientation regulate the epigenetic state of ribosomal RNA genes. Cold Spring Harb Symp Quant Biol (2011) 1.00
Sorting the nuclear proteome. Bioinformatics (2011) 0.92
Maternal Oct-4 is a potential key regulator of the developmental competence of mouse oocytes. BMC Dev Biol (2008) 0.92
Developmental expression of pluripotency determining factors in caprine embryos: novel pattern of NANOG protein localization in the nucleolus. Mol Reprod Dev (2006) 0.90
Incognito rRNA and rDNA in databases and libraries. Genome Res (1997) 0.88
Core transcription factors, Oct4, Sox2 and Nanog, individually form complexes with nucleophosmin (Npm1) to control embryonic stem (ES) cell fate determination. Aging (Albany NY) (2010) 0.87
Nuclear distribution of Oct-4 transcription factor in transcriptionally active and inactive mouse oocytes and its relation to RNA polymerase II and splicing factors. J Cell Biochem (2003) 0.86
WDR55 is a nucleolar modulator of ribosomal RNA synthesis, cell cycle progression, and teleost organ development. PLoS Genet (2008) 0.85
DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods (2006) 6.25
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 3.57
CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development (2009) 3.34
Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res (2009) 2.31
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet (2010) 2.20
Epigenomic enhancer profiling defines a signature of colon cancer. Science (2012) 2.15
Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res (2013) 2.14
Of mice and MEN1: Insulinomas in a conditional mouse knockout. Mol Cell Biol (2003) 2.12
Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. Nat Methods (2008) 2.02
Rapid and robust generation of functional oligodendrocyte progenitor cells from epiblast stem cells. Nat Methods (2011) 1.85
Molecular and phenotypic aspects of CHD7 mutation in CHARGE syndrome. Am J Med Genet A (2010) 1.82
ITCH K63-ubiquitinates the NOD2 binding protein, RIP2, to influence inflammatory signaling pathways. Curr Biol (2009) 1.34
Histone demethylase UTX and chromatin remodeler BRM bind directly to CBP and modulate acetylation of histone H3 lysine 27. Mol Cell Biol (2012) 1.20
Integrative genomic analysis of human ribosomal DNA. Nucleic Acids Res (2011) 1.18
Molecular pathology of the MEN1 gene. Ann N Y Acad Sci (2004) 1.16
CHD7 functions in the nucleolus as a positive regulator of ribosomal RNA biogenesis. Hum Mol Genet (2010) 1.13
The chromatin fingerprint of gene enhancer elements. J Biol Chem (2012) 1.08
Deep congenic analysis identifies many strong, context-dependent QTLs, one of which, Slc35b4, regulates obesity and glucose homeostasis. Genome Res (2011) 1.06
Role of canonical Wnt signaling/ß-catenin via Dermo1 in cranial dermal cell development. Development (2010) 1.03
Trithorax monomethylates histone H3K4 and interacts directly with CBP to promote H3K27 acetylation and antagonize Polycomb silencing. Development (2014) 0.97
Microarray analysis using amplified mRNA from laser capture microdissection of microscopic hepatocellular precancerous lesions and frozen hepatocellular carcinomas reveals unique and consistent gene expression profiles. Toxicol Pathol (2003) 0.94
Mutations in the CHD7 gene: the experience of a commercial laboratory. Genet Test Mol Biomarkers (2010) 0.93
Long ncRNA expression associates with tissue-specific enhancers. Cell Cycle (2015) 0.92
H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Genome Med (2012) 0.90
Distribution of menin-occupied regions in chromatin specifies a broad role of menin in transcriptional regulation. Neoplasia (2007) 0.89
Twist1 mediates repression of chondrogenesis by β-catenin to promote cranial bone progenitor specification. Development (2012) 0.87
CHD7 and retinoic acid signaling cooperate to regulate neural stem cell and inner ear development in mouse models of CHARGE syndrome. Hum Mol Genet (2013) 0.87
Temporal and spatial expression of CCN genes in zebrafish. Dev Dyn (2010) 0.84
Otitis media in a new mouse model for CHARGE syndrome with a deletion in the Chd7 gene. PLoS One (2012) 0.83
Knockdown of fbxl10/kdm2bb rescues chd7 morphant phenotype in a zebrafish model of CHARGE syndrome. Dev Biol (2013) 0.81
Functional studies of menin through genetic manipulation of the Men1 homolog in mice. Adv Exp Med Biol (2009) 0.79
Mutations in the noncoding genome. Curr Opin Pediatr (2015) 0.76