The chromatin fingerprint of gene enhancer elements.

Genome organization and long-range regulation of gene expression by enhancers. Curr Opin Cell Biol (2013) 1.63

Functional annotation of colon cancer risk SNPs. Nat Commun (2014) 1.19

De novo mutations in the genome organizer CTCF cause intellectual disability. Am J Hum Genet (2013) 1.01

The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages. Genes Dev (2014) 1.00

Transcriptional and epigenetic regulation of PPARγ expression during adipogenesis. Cell Biosci (2014) 0.98

Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes. Blood (2014) 0.95

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells. BMC Genomics (2014) 0.94

Evolution of transcriptional enhancers and animal diversity. Philos Trans R Soc Lond B Biol Sci (2013) 0.94

Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9. PLoS Pathog (2013) 0.90

Melanoma antigen-A11 (MAGE-A11) enhances transcriptional activity by linking androgen receptor dimers. J Biol Chem (2012) 0.87

A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Res (2015) 0.86

Enhancer turnover and conserved regulatory function in vertebrate evolution. Philos Trans R Soc Lond B Biol Sci (2013) 0.85

The interaction of MYC with the trithorax protein ASH2L promotes gene transcription by regulating H3K27 modification. Nucleic Acids Res (2014) 0.85

Identification of an enhancer that increases miR-200b~200a~429 gene expression in breast cancer cells. PLoS One (2013) 0.82

Epigenetics: the fine-tuner in inflammatory bowel disease? Curr Opin Gastroenterol (2013) 0.81

Cell-Type Specific Determinants of NRAMP1 Expression in Professional Phagocytes. Biology (Basel) (2013) 0.79

Human genetic variation within neural crest enhancers: molecular and phenotypic implications. Philos Trans R Soc Lond B Biol Sci (2013) 0.79

Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles. Nat Med (2016) 0.78

Identifying transcription start sites and active enhancer elements using BruUV-seq. Sci Rep (2015) 0.78

Chromatin Dynamics in the Regulation of CFTR Expression. Genes (Basel) (2015) 0.78

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture. Nucleic Acids Res (2016) 0.78

Variation in vertebrate cis-regulatory elements in evolution and disease. Transcription (2014) 0.77

pENCODE: a plant encyclopedia of DNA elements. Annu Rev Genet (2014) 0.77

Recruitment of transcription complexes to enhancers and the role of enhancer transcription. Biology (Basel) (2012) 0.77

Mutations in the noncoding genome. Curr Opin Pediatr (2015) 0.76

High Fractional Occupancy of a Tandem Maf Recognition Element and Its Role in Long-Range β-Globin Gene Regulation. Mol Cell Biol (2015) 0.75

Intragenic Locus in Human PIWIL2 Gene Shares Promoter and Enhancer Functions. PLoS One (2016) 0.75

Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction. Sci Rep (2017) 0.75

Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling. Elife (2017) 0.75

A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells. BMC Genomics (2015) 0.75

High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41

Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83

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

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell (2010) 23.97

A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes. Cell (1983) 20.32

A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene. Cell (1983) 18.86

A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature (2009) 18.39

ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38

Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28

Widespread transcription at neuronal activity-regulated enhancers. Nature (2010) 16.52

High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93

Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 15.13

CTCF: master weaver of the genome. Cell (2009) 15.09

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

Long noncoding RNAs with enhancer-like function in human cells. Cell (2010) 13.00

Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39

An oestrogen-receptor-alpha-bound human chromatin interactome. Nature (2009) 12.16

In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74

Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell (2009) 8.69

Regulation of chromatin by histone modifications. Cell Res (2011) 8.44

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res (2006) 7.72

Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet (2007) 7.61

Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet (2007) 6.92

A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet (2003) 6.82

A map of open chromatin in human pancreatic islets. Nat Genet (2010) 6.75

CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55

Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity (2010) 6.48

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature (2011) 6.10

A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol (2010) 6.01

Nucleosome dynamics define transcriptional enhancers. Nat Genet (2010) 5.94

Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93

H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet (2009) 5.82

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res (2005) 5.71

Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol Cell (2005) 5.38

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell (2011) 5.27

Functional and mechanistic diversity of distal transcription enhancers. Cell (2011) 5.22

The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev (2006) 4.94

Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science (2010) 4.72

ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res (2010) 4.50

Histone variants--ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol (2010) 4.45

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43

ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet (2010) 4.32

Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev (2007) 4.19

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res (2008) 4.11

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev (2009) 4.09

Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription. Mol Cell (1998) 4.03

Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. Mol Cell (2000) 3.75

Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science (2006) 3.59

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 3.57

Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet (2008) 3.55

The Foxa family of transcription factors in development and metabolism. Cell Mol Life Sci (2006) 3.47

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development (2009) 3.34

Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO J (2010) 3.25

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol (2010) 3.24

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A (2011) 3.18

CHD7 cooperates with PBAF to control multipotent neural crest formation. Nature (2010) 2.88

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. Genome Res (2009) 2.87

Histone modification: cause or cog? Trends Genet (2011) 2.85

Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development (2005) 2.56

Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes. Nucleic Acids Res (2010) 2.37

Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm. Cold Spring Harb Symp Quant Biol (2008) 2.34

Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res (2009) 2.31

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res (2007) 2.27

CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet (2010) 2.20

A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res (2008) 2.10

H2A.Z: view from the top. Structure (2008) 2.07

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res (2011) 2.07

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Res (2011) 2.00

DNA methylation status predicts cell type-specific enhancer activity. EMBO J (2011) 1.98

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers. Genome Res (2011) 1.92

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res (2010) 1.90

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res (2009) 1.89

Germline nonsense mutation and somatic inactivation of SMARCA4/BRG1 in a family with rhabdoid tumor predisposition syndrome. Am J Hum Genet (2010) 1.83

Molecular and phenotypic aspects of CHD7 mutation in CHARGE syndrome. Am J Med Genet A (2010) 1.82

Genomics of long-range regulatory elements. Annu Rev Genomics Hum Genet (2010) 1.75

Characterization of mammary tumors from Brg1 heterozygous mice. Oncogene (2007) 1.70

The nucleosome map of the mammalian liver. Nat Struct Mol Biol (2011) 1.47

The chromatin-remodeling enzyme BRG1 coordinates CIITA induction through many interdependent distal enhancers. Nat Immunol (2008) 1.44

PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers. Proc Natl Acad Sci U S A (2011) 1.30

Aberrant expression of SWI/SNF catalytic subunits BRG1/BRM is associated with tumor development and increased invasiveness in prostate cancers. Prostate (2007) 1.28

HHMD: the human histone modification database. Nucleic Acids Res (2009) 1.27

Genome-wide assessment of differential roles for p300 and CBP in transcription regulation. Nucleic Acids Res (2010) 1.25

Massive parallel DNA pyrosequencing analysis of the tumor suppressor BRG1/SMARCA4 in lung primary tumors. Hum Mutat (2010) 1.24

Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) 1.23

Dynamic BRG1 recruitment during T helper differentiation and activation reveals distal regulatory elements. Mol Cell Biol (2011) 1.17

Processing the H3K36me3 signature. Nat Genet (2009) 1.10

Genetic and expressional alterations of CHD genes in gastric and colorectal cancers. Histopathology (2011) 1.09

BRG1 expression is increased in human cutaneous melanoma. Br J Dermatol (2010) 1.08

Genome-wide identification of conserved regulatory function in diverged sequences. Genome Res (2011) 1.07

Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease. Genome Med (2011) 1.03

DNA methylation of intronic enhancers directs tissue-specific expression of steroidogenic factor 1/adrenal 4 binding protein (SF-1/Ad4BP). Endocrinology (2011) 1.01

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

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

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

Genomic characterization of the mouse ribosomal DNA locus. G3 (Bethesda) (2014) 0.80

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