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

High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res (2009) 5.11

Impact of chromatin structures on DNA processing for genomic analyses. PLoS One (2009) 2.63

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A (2013) 2.33

Epigenetic instability due to defective replication of structured DNA. Mol Cell (2010) 1.86

Global position analysis of the Pseudomonas aeruginosa quorum-sensing transcription factor LasR. Mol Microbiol (2009) 1.55

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

Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast. Proc Natl Acad Sci U S A (2011) 1.12

Ume6 transcription factor is part of a signaling cascade that regulates autophagy. Proc Natl Acad Sci U S A (2012) 1.08

Tandem ChoRE and CCAAT motifs and associated factors regulate Txnip expression in response to glucose or adenosine-containing molecules. PLoS One (2009) 1.02

Transforming growth factor-beta1 up-regulation of human alpha(1)(I) collagen is mediated by Sp1 and Smad2 transacting factors. DNA Cell Biol (2009) 1.02

Signal transducers and activators of transcription 3 (STAT3) directly regulates cytokine-induced fascin expression and is required for breast cancer cell migration. J Biol Chem (2011) 0.98

Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization. Nucleic Acids Res (2011) 0.96

Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction. Nucleic Acids Res (2010) 0.95

A combinatorial mechanism for determining the specificity of E2F activation and repression. Oncogene (2009) 0.94

Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes. J Biol Chem (2015) 0.94

Direct regulation of nucleosome density by the conserved AAA-ATPase Yta7. Proc Natl Acad Sci U S A (2011) 0.92

Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing. Proc Natl Acad Sci U S A (2011) 0.92

High-resolution mapping studies of chromatin and gene regulatory elements. Epigenomics (2009) 0.91

Cap completion and C-terminal repeat domain kinase recruitment underlie the initiation-elongation transition of RNA polymerase II. Mol Cell Biol (2013) 0.91

A nuclear role for the respiratory enzyme CLK-1 in regulating mitochondrial stress responses and longevity. Nat Cell Biol (2015) 0.90

Chromatin structure and expression of a gene transcribed by RNA polymerase III are independent of H2A.Z deposition. Mol Cell Biol (2008) 0.89

The molecular topography of silenced chromatin in Saccharomyces cerevisiae. Genes Dev (2014) 0.89

Anacardic acid inhibits estrogen receptor alpha-DNA binding and reduces target gene transcription and breast cancer cell proliferation. Mol Cancer Ther (2010) 0.86

Nej1 recruits the Srs2 helicase to DNA double-strand breaks and supports repair by a single-strand annealing-like mechanism. Proc Natl Acad Sci U S A (2009) 0.85

Expanded CAG/CTG repeat DNA induces a checkpoint response that impacts cell proliferation in Saccharomyces cerevisiae. PLoS Genet (2011) 0.84

The APSES transcription factor Efg1 is a global regulator that controls morphogenesis and biofilm formation in Candida parapsilosis. Mol Microbiol (2013) 0.84

Differential phosphorylation of a regulatory subunit of protein kinase CK2 by target of rapamycin complex 1 signaling and the Cdc-like kinase Kns1. J Biol Chem (2015) 0.84

The yeast Snt2 protein coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress. Mol Cell Biol (2013) 0.83

Evolutionary expansion of a regulatory network by counter-silencing. Nat Commun (2014) 0.82

Distinct roles of the Salmonella enterica serovar Typhimurium CyaY and YggX proteins in the biosynthesis and repair of iron-sulfur clusters. Infect Immun (2014) 0.81

YY1 acts as a transcriptional activator of Hoxa5 gene expression in mouse organogenesis. PLoS One (2014) 0.81

The transcription factors Tec1 and Ste12 interact with coregulators Msa1 and Msa2 to activate adhesion and multicellular development. Mol Cell Biol (2014) 0.81

Transcriptional activation by the Mixl1 homeodomain protein in differentiating mouse embryonic stem cells. Stem Cells (2009) 0.81

Maintenance of nucleosomal balance in cis by conserved AAA-ATPase Yta7. Genetics (2014) 0.80

On the Mechanism of Gene Silencing in Saccharomyces cerevisiae. G3 (Bethesda) (2015) 0.80

Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex. Elife (2016) 0.79

Control of endothelin-a receptor expression by progesterone is enhanced by synergy with Gata2. Mol Endocrinol (2013) 0.78

Regulatory mechanisms that prevent re-initiation of DNA replication can be locally modulated at origins by nearby sequence elements. PLoS Genet (2014) 0.77

Coordinated gene regulation in the initial phase of salt stress adaptation. J Biol Chem (2015) 0.76

Histone Deacetylases with Antagonistic Roles in Saccharomyces cerevisiae Heterochromatin Formation. Genetics (2016) 0.76

Identifying TF-MiRNA Regulatory Relationships Using Multiple Features. PLoS One (2015) 0.76

Characterization of the Mouse and Human Monoacylglycerol O-Acyltransferase 1 (Mogat1) Promoter in Human Kidney Proximal Tubule and Rat Liver Cells. PLoS One (2016) 0.75

APOE genotype-function relationship: evidence of -491 A/T promoter polymorphism modifying transcription control but not type 2 diabetes risk. PLoS One (2011) 0.75

Evolution and Functional Trajectory of Sir1 in Gene Silencing. Mol Cell Biol (2016) 0.75

BET inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps. J Biol Chem (2017) 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

Retrovirus resistance factors Ref1 and Lv1 are species-specific variants of TRIM5alpha. Proc Natl Acad Sci U S A (2004) 5.15

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

p63 and p73 are required for p53-dependent apoptosis in response to DNA damage. Nature (2002) 4.56

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

Tumor predisposition in mice mutant for p63 and p73: evidence for broader tumor suppressor functions for the p53 family. Cancer Cell (2005) 4.14

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

p63 protects the female germ line during meiotic arrest. Nature (2006) 3.98

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

Human tripartite motif 5alpha domains responsible for retrovirus restriction activity and specificity. J Virol (2005) 3.54

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

REDD1, a developmentally regulated transcriptional target of p63 and p53, links p63 to regulation of reactive oxygen species. Mol Cell (2002) 3.29

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

An Fcγ receptor-dependent mechanism drives antibody-mediated target-receptor signaling in cancer cells. Cancer Cell (2011) 2.14

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

Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr Protoc Cell Biol (2004) 1.98

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

A novel FMR1 PCR method for the routine detection of low abundance expanded alleles and full mutations in fragile X syndrome. Clin Chem (2010) 1.86

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

A C-terminal inhibitory domain controls the activity of p63 by an intramolecular mechanism. Mol Cell Biol (2002) 1.73

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

An information-rich CGG repeat primed PCR that detects the full range of fragile X expanded alleles and minimizes the need for southern blot analysis. J Mol Diagn (2010) 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