Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo.

Acetylation is indispensable for p53 activation. Cell (2008) 5.70

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22

Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83

Genetic analysis of variation in transcription factor binding in yeast. Nature (2010) 2.69

Epigenetic silencing mediates mitochondria stress-induced longevity. Cell Metab (2013) 2.03

Myc represses primitive endoderm differentiation in pluripotent stem cells. Cell Stem Cell (2010) 1.90

Epigenetic and conventional regulation is distributed among activators of FLO11 allowing tuning of population-level heterogeneity in its expression. PLoS Genet (2009) 1.88

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc (2013) 1.73

Maintenance of the DNA-damage checkpoint requires DNA-damage-induced mediator protein oligomerization. Mol Cell (2009) 1.73

The Notch target Hes1 directly modulates Gli1 expression and Hedgehog signaling: a potential mechanism of therapeutic resistance. Clin Cancer Res (2010) 1.58

The next-generation sequencing technology and application. Protein Cell (2010) 1.52

Mechanisms of specificity in neuronal activity-regulated gene transcription. Prog Neurobiol (2011) 1.49

A regulatory role for repeated decoy transcription factor binding sites in target gene expression. Mol Syst Biol (2012) 1.35

Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects. PLoS Genet (2011) 1.26

Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines. Nucleic Acids Res (2012) 1.17

A reexamination of information theory-based methods for DNA-binding site identification. BMC Bioinformatics (2009) 1.12

Replication stress checkpoint signaling controls tRNA gene transcription. Nat Struct Mol Biol (2010) 1.06

Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system. Mol Microbiol (2012) 1.02

A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data. Nucleic Acids Res (2014) 0.99

The yeast cap binding complex modulates transcription factor recruitment and establishes proper histone H3K36 trimethylation during active transcription. Mol Cell Biol (2012) 0.96

Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites. PLoS Comput Biol (2010) 0.95

Multilevel support vector regression analysis to identify condition-specific regulatory networks. Bioinformatics (2010) 0.93

Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data. PLoS One (2012) 0.91

Chromatin immunoprecipitation (ChIP): revisiting the efficacy of sample preparation, sonication, quantification of sheared DNA, and analysis via PCR. PLoS One (2011) 0.91

Formalin can alter the intracellular localization of some transcription factors in Saccharomyces cerevisiae. FEMS Yeast Res (2008) 0.90

An extracytoplasmic function sigma factor-mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores. J Bacteriol (2011) 0.90

RAP: accurate and fast motif finding based on protein-binding microarray data. J Comput Biol (2013) 0.90

Peroxisome proliferator-activated receptor γ-dependent regulation of lipolytic nodes and metabolic flexibility. Mol Cell Biol (2012) 0.87

Decoding the trans-histone crosstalk: methods to analyze H2B ubiquitination, H3 methylation and their regulatory factors. Methods (2011) 0.85

Molecular genomic research designs. Annu Rev Nurs Res (2011) 0.83

Timing of transcriptional quiescence during gametogenesis is controlled by global histone H3K4 demethylation. Dev Cell (2012) 0.83

Essential role of the iron-sulfur cluster binding domain of the primase regulatory subunit Pri2 in DNA replication initiation. Protein Cell (2015) 0.82

Chromatin remodeling by the SWI/SNF complex is essential for transcription mediated by the yeast cell wall integrity MAPK pathway. Mol Biol Cell (2012) 0.82

Integrative radiation systems biology. Radiat Oncol (2014) 0.81

The 9-1-1 checkpoint clamp coordinates resection at DNA double strand breaks. Nucleic Acids Res (2015) 0.81

HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data. BMC Bioinformatics (2010) 0.81

Analysis of RXR/THR and RXR/PPARG2 heterodimerization by bioluminescence resonance energy transfer (BRET). PLoS One (2013) 0.80

Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath. PLoS One (2015) 0.80

Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus. BMC Genomics (2016) 0.79

Combinatorial Cis-regulation in Saccharomyces Species. G3 (Bethesda) (2016) 0.79

Derepression of INO1 transcription requires cooperation between the Ino2p-Ino4p heterodimer and Cbf1p and recruitment of the ISW2 chromatin-remodeling complex. Eukaryot Cell (2010) 0.79

E2F4 Program Is Predictive of Progression and Intravesical Immunotherapy Efficacy in Bladder Cancer. Mol Cancer Res (2015) 0.79

The effect of an intervening promoter nucleosome on gene expression. PLoS One (2013) 0.78

DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems. J Vis Exp (2014) 0.78

Inhibition of corticosteroid-binding globulin gene expression by glucocorticoids involves C/EBPβ. PLoS One (2014) 0.78

"Non-canonical protein-DNA interactions identified by ChIP are not artifacts": response. BMC Genomics (2013) 0.77

HOXB4 Gene Expression Is Regulated by CDX2 in Intestinal Epithelial Cells. PLoS One (2016) 0.75

PIPE-chipSAD: A Pipeline for the Analysis of High Density Arrays of Bacterial Transcriptomes. Front Mol Biosci (2016) 0.75

Polymerases ε and ∂ repair dysfunctional telomeres facilitated by salt. Nucleic Acids Res (2016) 0.75

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

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell (2004) 16.15

Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell (2003) 11.78

An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell (2009) 10.09

Metformin selectively targets cancer stem cells, and acts together with chemotherapy to block tumor growth and prolong remission. Cancer Res (2009) 6.74

TREX is a conserved complex coupling transcription with messenger RNA export. Nature (2002) 6.53

Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell (2005) 6.17

STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer. Mol Cell (2010) 5.67

Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol (2002) 5.53

Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99

Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell (2005) 4.77

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51

An HNF4α-miRNA inflammatory feedback circuit regulates hepatocellular oncogenesis. Cell (2011) 4.29

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08

Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev (2002) 4.07

Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol Cell Biol (2004) 4.06

A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases. Cancer Cell (2010) 4.02

Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell (2005) 4.00

Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev (2002) 3.93

Loss of miR-200 inhibition of Suz12 leads to polycomb-mediated repression required for the formation and maintenance of cancer stem cells. Mol Cell (2010) 3.53

Inducible formation of breast cancer stem cells and their dynamic equilibrium with non-stem cancer cells via IL6 secretion. Proc Natl Acad Sci U S A (2011) 3.42

Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J Biol Chem (2002) 3.14

Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc Natl Acad Sci U S A (2003) 3.09

The Rtf1 component of the Paf1 transcriptional elongation complex is required for ubiquitination of histone H2B. J Biol Chem (2003) 3.08

The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol Cell Biol (2003) 3.03

A nuclear receptor-like pathway regulating multidrug resistance in fungi. Nature (2008) 3.00

The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell (2006) 2.99

SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature (2012) 2.96

Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol Cell (2002) 2.93

Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90

A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell (2012) 2.86

Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83

Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II. Mol Cell (2006) 2.71

Metformin decreases the dose of chemotherapy for prolonging tumor remission in mouse xenografts involving multiple cancer cell types. Cancer Res (2011) 2.53

MicroRNAs differentially regulated by Akt isoforms control EMT and stem cell renewal in cancer cells. Sci Signal (2009) 2.38

The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature (2004) 2.37

Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Mol Biol (2006) 2.30

A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell (2004) 2.27

Activator-specific recruitment of Mediator in vivo. Nat Struct Mol Biol (2006) 2.25

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol (2010) 2.15

Dynamics of global histone acetylation and deacetylation in vivo: rapid restoration of normal histone acetylation status upon removal of activators and repressors. Genes Dev (2002) 2.14

Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol (2004) 2.13

Metformin inhibits the inflammatory response associated with cellular transformation and cancer stem cell growth. Proc Natl Acad Sci U S A (2012) 2.11

MAP kinase-mediated stress relief that precedes and regulates the timing of transcriptional induction. Cell (2004) 2.09

Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev (2005) 2.06

Epigenomics: a roadmap, but to where? Science (2008) 1.99

HBO1 histone acetylase activity is essential for DNA replication licensing and inhibited by Geminin. Mol Cell (2010) 1.95

The stress-activated Hog1 kinase is a selective transcriptional elongation factor for genes responding to osmotic stress. Mol Cell (2006) 1.85

Heterochromatin formation involves changes in histone modifications over multiple cell generations. EMBO J (2005) 1.82

Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo. Nucleic Acids Res (2004) 1.81

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. Genome Biol (2005) 1.80

The transition from transcriptional initiation to elongation. Curr Opin Genet Dev (2008) 1.78

Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol Cell (2002) 1.76

The Swi/Snf complex is important for histone eviction during transcriptional activation and RNA polymerase II elongation in vivo. Mol Cell Biol (2007) 1.72

HBO1 histone acetylase is a coactivator of the replication licensing factor Cdt1. Genes Dev (2008) 1.67

Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J Bacteriol (2004) 1.65

JNK1 phosphorylation of Cdt1 inhibits recruitment of HBO1 histone acetylase and blocks replication licensing in response to stress. Mol Cell (2011) 1.61

Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr Protoc Mol Biol (2005) 1.58

Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae. Mol Cell Biol (2004) 1.56

Akt2 regulates all Akt isoforms and promotes resistance to hypoxia through induction of miR-21 upon oxygen deprivation. Cancer Res (2011) 1.48

Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization. Mol Microbiol (2007) 1.47

The VP16 activation domain interacts with multiple transcriptional components as determined by protein-protein cross-linking in vivo. J Biol Chem (2002) 1.47

Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae. Eukaryot Cell (2005) 1.42

An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol Cell Biol (2006) 1.39

Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc Natl Acad Sci U S A (2010) 1.37

Cellular stress alters the transcriptional properties of promoter-bound Mot1-TBP complexes. Mol Cell (2004) 1.36

High-throughput sequencing reveals a simple model of nucleosome energetics. Proc Natl Acad Sci U S A (2010) 1.34

Mot1 associates with transcriptionally active promoters and inhibits association of NC2 in Saccharomyces cerevisiae. Mol Cell Biol (2002) 1.34

Where does mediator bind in vivo? PLoS One (2009) 1.33

The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein. Genes Dev (2011) 1.30

Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucleic Acids Res (2008) 1.23

An integrated transcriptional regulatory circuit that reinforces the breast cancer stem cell state. Proc Natl Acad Sci U S A (2012) 1.22

Targeted recruitment of Rpd3 histone deacetylase represses transcription by inhibiting recruitment of Swi/Snf, SAGA, and TATA binding protein. Mol Cell Biol (2002) 1.22

Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments. BMC Bioinformatics (2006) 1.20

NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. Genome Res (2013) 1.15

Inhibition of miR-193a expression by Max and RXRα activates K-Ras and PLAU to mediate distinct aspects of cellular transformation. Cancer Res (2011) 1.15

Genome-wide location analysis of the stress-activated MAP kinase Hog1 in yeast. Methods (2006) 1.13

Splitting of H3-H4 tetramers at transcriptionally active genes undergoing dynamic histone exchange. Proc Natl Acad Sci U S A (2011) 1.09

Association of RNA polymerase with transcribed regions in Escherichia coli. Proc Natl Acad Sci U S A (2004) 1.02

Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts. Proc Natl Acad Sci U S A (2013) 0.99

Differential gene regulation by selective association of transcriptional coactivators and bZIP DNA-binding domains. Mol Cell Biol (2006) 0.99

Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo. PLoS One (2010) 0.98

Expanding the repertoire of plasmids for PCR-mediated epitope tagging in yeast. Yeast (2008) 0.96

Extensive divergence of yeast stress responses through transitions between induced and constitutive activation. Proc Natl Acad Sci U S A (2011) 0.93

Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes. Cell Rep (2012) 0.92

Differential analysis for high density tiling microarray data. BMC Bioinformatics (2007) 0.87

Analysis of protein co-occupancy by quantitative sequential chromatin immunoprecipitation. Curr Protoc Mol Biol (2005) 0.87

Iwr1 protein is important for preinitiation complex formation by all three nuclear RNA polymerases in Saccharomyces cerevisiae. PLoS One (2011) 0.84

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.". Nat Struct Mol Biol (2010) 0.80

Conditional depletion of nuclear proteins by the Anchor Away system. Curr Protoc Mol Biol (2011) 0.79

[Histone H4 lysine 16 acetylation: from genome regulation to tumoral progression]. Med Sci (Paris) (2007) 0.77

Construction of mutant alleles in Saccharomyces cerevisiae without cloning: overview and the delitto perfetto method. Curr Protoc Mol Biol (2013) 0.77

Mapping 3' mRNA isoforms on a genomic scale. Curr Protoc Mol Biol (2015) 0.75

Defining in vivo targets of nuclear proteins by chromatin immunoprecipitation and microarray analysis. Curr Protoc Mol Biol (2004) 0.75