Published in Dev Biol on December 16, 2009
Mediator and cohesin connect gene expression and chromatin architecture. Nature (2010) 14.34
A unique chromatin signature uncovers early developmental enhancers in humans. Nature (2010) 14.02
An atlas of active enhancers across human cell types and tissues. Nature (2014) 6.57
Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet (2011) 5.27
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 3.57
CTCF-binding elements mediate control of V(D)J recombination. Nature (2011) 2.62
Rapid evolutionary rewiring of a structurally constrained eye enhancer. Curr Biol (2011) 1.98
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet (2011) 1.94
Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. Cell Stem Cell (2012) 1.80
Genome-wide significant locus of beta-trace protein, a novel kidney function biomarker, identified in European and African Americans. Nephrol Dial Transplant (2013) 1.56
Long non-coding RNAs and enhancers. Curr Opin Genet Dev (2011) 1.52
Enhancers as information integration hubs in development: lessons from genomics. Trends Genet (2012) 1.52
Chromatin insulators: linking genome organization to cellular function. Mol Cell (2013) 1.51
Understanding the temporal codes of intra-cellular signals. Curr Opin Genet Dev (2010) 1.48
A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Rep (2012) 1.39
Cohesin mediates chromatin interactions that regulate mammalian β-globin expression. J Biol Chem (2011) 1.29
Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation. Blood (2010) 1.27
Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding. Mol Cell Biol (2012) 1.15
Transcription factor binding predicts histone modifications in human cell lines. Proc Natl Acad Sci U S A (2014) 1.09
Global analysis of DNA methylation in early-stage liver fibrosis. BMC Med Genomics (2012) 1.07
Multiple Wnt/ß-catenin responsive enhancers align with the MYC promoter through long-range chromatin loops. PLoS One (2011) 1.05
Memories of lost enhancers. Genes Dev (2010) 1.05
Identification of biologically relevant enhancers in human erythroid cells. J Biol Chem (2013) 1.03
Twist1 directly regulates genes that promote cell proliferation and migration in developing heart valves. PLoS One (2011) 0.96
Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes. Blood (2014) 0.95
An RNA-independent linkage of noncoding transcription to long-range enhancer function. Mol Cell Biol (2012) 0.91
Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. Mob DNA (2014) 0.91
Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors. Proc Natl Acad Sci U S A (2013) 0.89
SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps. PLoS Comput Biol (2015) 0.88
The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression. Hum Mol Genet (2013) 0.87
Epigenetic modifications unlock the milk protein gene loci during mouse mammary gland development and differentiation. PLoS One (2013) 0.86
DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer. Nat Commun (2015) 0.86
From remote enhancers to gene regulation: charting the genome's regulatory landscapes. Philos Trans R Soc Lond B Biol Sci (2013) 0.86
The insulator protein Suppressor of Hairy-wing is an essential transcriptional repressor in the Drosophila ovary. Development (2013) 0.83
Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. Front Plant Sci (2013) 0.83
Impact of nuclear organization and dynamics on epigenetic regulation in the central nervous system: implications for neurological disease states. Ann N Y Acad Sci (2010) 0.82
Progress and challenges in bioinformatics approaches for enhancer identification. Brief Bioinform (2015) 0.82
Genome-wide profiling identifies a subset of methamphetamine (METH)-induced genes associated with METH-induced increased H4K5Ac binding in the rat striatum. BMC Genomics (2013) 0.82
Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA. Gene Regul Syst Bio (2012) 0.80
Functional analysis of conserved sequences within a temporally restricted neural precursor cell enhancer. Mech Dev (2011) 0.80
CTCF-dependent chromatin insulator as a built-in attenuator of angiogenesis. Transcription (2012) 0.80
FOXC1 is involved in ERα silencing by counteracting GATA3 binding and is implicated in endocrine resistance. Oncogene (2016) 0.79
The Drosophila gypsy insulator supports transvection in the presence of the vestigial enhancer. PLoS One (2013) 0.78
Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming. Genes (Basel) (2015) 0.78
PEDLA: predicting enhancers with a deep learning-based algorithmic framework. Sci Rep (2016) 0.77
PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c. Nucleic Acids Res (2016) 0.76
Regulatory modules function in a non-autonomous manner to control transcription of the mbp gene. Nucleic Acids Res (2010) 0.76
Applying CRISPR-Cas9 tools to identify and characterize transcriptional enhancers. Nat Rev Mol Cell Biol (2016) 0.76
Unexpected DNA context-dependence identifies a new determinant of Chi recombination hotspots. Nucleic Acids Res (2016) 0.76
Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome. DNA Res (2016) 0.76
High resolution mapping of enhancer-promoter interactions. PLoS One (2015) 0.75
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. Elife (2017) 0.75
Enhancers. Wiley Interdiscip Rev Dev Biol (2012) 0.75
Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions. BMC Syst Biol (2016) 0.75
Embryonic Stem Cell (ES)-Specific Enhancers Specify the Expression Potential of ES Genes in Cancer. PLoS Genet (2016) 0.75
A gene-specific non-enhancer sequence is critical for expression from the promoter of the small heat shock protein gene αB-crystallin. Hum Genomics (2014) 0.75
Generation of transgenic mouse fluorescent reporter lines for studying hematopoietic development. Methods Mol Biol (2014) 0.75
Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover. Bioessays (2016) 0.75
High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti. BMC Genomics (2016) 0.75
EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm. Sci Rep (2016) 0.75
Single-cell profiling reveals that eRNA accumulation at enhancer-promoter loops is not required to sustain transcription. Nucleic Acids Res (2016) 0.75
Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data. Nucleic Acids Res (2016) 0.75
Systematic targeted integration to study Albumin gene control elements. PLoS One (2011) 0.75
Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer's disease. PLoS Genet (2017) 0.75
Scc2/Nipbl hops between chromosomal cohesin rings after loading. Elife (2017) 0.75
Study of the effects of enhancer and insulator on the chromatin structure in Drosophila melanogaster. Dokl Biochem Biophys (2011) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
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
Capturing chromosome conformation. Science (2002) 23.93
Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell (1981) 20.72
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Position-independent, high-level expression of the human beta-globin gene in transgenic mice. Cell (1987) 15.79
The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. Nucleic Acids Res (1981) 15.12
Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell (2002) 11.35
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet (2006) 11.02
The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell (1999) 9.74
Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet (2004) 9.57
Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol (2009) 9.29
Interchromosomal associations between alternatively expressed loci. Nature (2005) 7.45
Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet (2006) 7.18
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Insulators: exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet (2006) 6.43
CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev (2006) 6.32
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet (2000) 5.88
We gather together: insulators and genome organization. Curr Opin Genet Dev (2007) 5.81
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell (2005) 5.77
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
The beta-globin nuclear compartment in development and erythroid differentiation. Nat Genet (2003) 5.54
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22
Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol (2004) 4.67
The active spatial organization of the beta-globin locus requires the transcription factor EKLF. Genes Dev (2004) 4.04
Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene (1997) 3.77
Active RNA polymerases are localized within discrete transcription "factories' in human nuclei. J Cell Sci (1996) 3.16
Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Mol Cell (2000) 3.03
Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J (2007) 2.99
Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol (2007) 2.72
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet (2008) 2.67
The beta -globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation. Genes Dev (2003) 2.65
Biochemical mechanisms of gene regulation by polycomb group protein complexes. Curr Opin Genet Dev (2009) 2.63
Long-range chromosomal interactions and gene regulation. Mol Biosyst (2008) 2.56
Distant liaisons: long-range enhancer-promoter interactions in Drosophila. Curr Opin Genet Dev (1999) 2.50
Locus control regions: coming of age at a decade plus. Trends Genet (1999) 2.46
Locus control region function and heterochromatin-induced position effect variegation. Science (1996) 2.42
A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res (2008) 2.10
Chip, a widely expressed chromosomal protein required for segmentation and activity of a remote wing margin enhancer in Drosophila. Genes Dev (1997) 2.07
Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus. Mol Cell (2007) 2.05
Similar active genes cluster in specialized transcription factories. J Cell Biol (2008) 2.05
Genetic and molecular analysis of the gypsy chromatin insulator of Drosophila. Proc Natl Acad Sci U S A (1996) 1.94
Dependence of enhancer-mediated transcription of the immunoglobulin mu gene on nuclear matrix attachment regions. Science (1994) 1.91
Synthetic human beta-globin 5'HS2 constructs function as locus control regions only in multicopy transgene concatamers. EMBO J (1993) 1.77
USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier. Mol Cell Biol (2007) 1.68
Flanking HS-62.5 and 3' HS1, and regions upstream of the LCR, are not required for beta-globin transcription. Blood (2006) 1.65
The murine beta-globin locus control region regulates the rate of transcription but not the hyperacetylation of histones at the active genes. Proc Natl Acad Sci U S A (2001) 1.41
Cohesin, gene expression and development: lessons from Drosophila. Chromosome Res (2009) 1.35
'Insulator bodies' are aggregates of proteins but not of insulators. EMBO Rep (2008) 1.11
The activity of the scs and scs' insulator elements is not dependent on chromosomal context. Mol Cell Biol (1997) 1.10
Dissecting a locus control region: facilitation of enhancer function by extended enhancer-flanking sequences. Mol Cell Biol (1995) 1.08
Variegated expression of the endogenous immunoglobulin heavy-chain gene in the absence of the intronic locus control region. Mol Cell Biol (1999) 1.03
A unique role for enhancers is revealed during early mouse development. Bioessays (1995) 1.00
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster. BMC Genomics (2009) 0.84
One thousand and one ways of making functionally similar transcriptional enhancers. Bioessays (2008) 0.82
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Controlling the double helix. Nature (2003) 8.61
The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev (2004) 7.57
An expansive human regulatory lexicon encoded in transcription factor footprints. Nature (2012) 7.27
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell (2005) 5.77
Functional and mechanistic diversity of distal transcription enhancers. Cell (2011) 5.22
Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet (2002) 4.68
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol (2004) 4.00
The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev (2006) 3.91
Developmental and species-divergent globin switching are driven by BCL11A. Nature (2009) 3.49
Form follows function: The genomic organization of cellular differentiation. Genes Dev (2004) 3.20
A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locus. Mol Cell Biol (2003) 3.09
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A (2004) 2.66
The beta -globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation. Genes Dev (2003) 2.65
A functional element necessary for fetal hemoglobin silencing. N Engl J Med (2011) 2.25
An unmethylated 3' promoter-proximal region is required for efficient transcription initiation. PLoS Genet (2007) 2.11
Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus. Mol Cell (2007) 2.05
Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat Struct Mol Biol (2003) 2.00
Heme regulates the dynamic exchange of Bach1 and NF-E2-related factors in the Maf transcription factor network. Proc Natl Acad Sci U S A (2004) 1.92
Gene order and dynamic domains. Science (2004) 1.86
The emergence of lineage-specific chromosomal topologies from coordinate gene regulation. Proc Natl Acad Sci U S A (2009) 1.78
On emerging nuclear order. J Cell Biol (2011) 1.77
Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol (2007) 1.77
A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements. Chromosome Res (2003) 1.67
Flanking HS-62.5 and 3' HS1, and regions upstream of the LCR, are not required for beta-globin transcription. Blood (2006) 1.65
DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent de novo methylation. Mol Cell Biol (2002) 1.57
ChIPs of the beta-globin locus: unraveling gene regulation within an active domain. Curr Opin Genet Dev (2002) 1.45
Bivalent domains enforce transcriptional memory of DNA methylated genes in cancer cells. Proc Natl Acad Sci U S A (2008) 1.36
Replication initiation patterns in the beta-globin loci of totipotent and differentiated murine cells: evidence for multiple initiation regions. Mol Cell Biol (2002) 1.32
The human beta-globin replication initiation region consists of two modular independent replicators. Mol Cell Biol (2004) 1.28
Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation. Blood (2010) 1.27
Molecular basis for chromatin binding and regulation of MLL5. Proc Natl Acad Sci U S A (2013) 1.15
The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. Elife (2014) 1.13
Transcriptional interference among the murine beta-like globin genes. Blood (2006) 1.06
Dynamics and control of state-dependent networks for probing genomic organization. Proc Natl Acad Sci U S A (2011) 1.05
The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation. Blood (2012) 1.04
Deletion of the core region of 5' HS2 of the mouse beta-globin locus control region reveals a distinct effect in comparison with human beta-globin transgenes. Blood (2005) 0.99
H3 K79 dimethylation marks developmental activation of the beta-globin gene but is reduced upon LCR-mediated high-level transcription. Blood (2008) 0.98
UpSET recruits HDAC complexes and restricts chromatin accessibility and acetylation at promoter regions. Cell (2012) 0.96
Something silent this way forms: the functional organization of the repressive nuclear compartment. Annu Rev Cell Dev Biol (2013) 0.95
Dido3 PHD modulates cell differentiation and division. Cell Rep (2013) 0.91
Histone hyperacetylation within the beta-globin locus is context-dependent and precedes high-level gene expression. Blood (2009) 0.89
Chromatin insulation by a transcriptional activator. Proc Natl Acad Sci U S A (2003) 0.87
Networking the nucleus. Mol Syst Biol (2010) 0.85
The nucleus inside out--through a rod darkly. Cell (2009) 0.82
Nucleolar tethering mediates pairing between the IgH and Myc loci. Nucleus (2014) 0.81
Functional redundancy in the nuclear compartmentalization of the late-replicating genome. Nucleus (2014) 0.80
TRAPping enhancer function. Nat Genet (2002) 0.80
When untethered, something silent inside comes. Nucleus (2013) 0.79
What can systems theory of networks offer to biology? PLoS Comput Biol (2012) 0.79
The undiscovered country: chromosome territories and the organization of transcription. Dev Cell (2002) 0.78
UpSET-ting the balance: modulating open chromatin features in metazoan genomes. Fly (Austin) (2013) 0.76
Losing control: cancer's catastrophic transition. Nucleus (2011) 0.76
Getting connected in the globin interactome. Nat Genet (2010) 0.76