Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

[1]  Song Liu,et al.  Alterations in chromatin accessibility and DNA methylation in clear cell renal cell carcinoma , 2014, Oncogene.

[2]  B. Mueller‐Roeber,et al.  A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana. , 2014, Journal of integrative plant biology.

[3]  Joel S Parker,et al.  Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects , 2014, Genome research.

[4]  P. Giresi,et al.  Addendum: Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA , 2014, Nature Protocols.

[5]  D. J. McKay,et al.  A common set of DNA regulatory elements shapes Drosophila appendages. , 2013, Developmental cell.

[6]  Diego Mauricio Riaño-Pachón,et al.  Genome-Wide Identification of Regulatory Elements and Reconstruction of Gene Regulatory Networks of the Green Alga Chlamydomonas reinhardtii under Carbon Deprivation , 2013, PloS one.

[7]  J. Lieb,et al.  The Open Chromatin Landscape of Kaposi's Sarcoma-Associated Herpesvirus , 2013, Journal of Virology.

[8]  Thomas Whitington,et al.  Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites , 2013, Cell.

[9]  Jeong Hoon Kim,et al.  CCAR1 promotes chromatin loading of androgen receptor (AR) transcription complex by stabilizing the association between AR and GATA2 , 2013, Nucleic acids research.

[10]  C. Rossetto,et al.  Cis and Trans Acting Factors Involved in Human Cytomegalovirus Experimental and Natural Latent Infection of CD14 (+) Monocytes and CD34 (+) Cells , 2013, PLoS pathogens.

[11]  Barbora Malecova,et al.  Epigenetic reprogramming of human embryonic stem cells into skeletal muscle cells and generation of contractile myospheres. , 2013, Cell reports.

[12]  Sebastian M. Armasu,et al.  Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer , 2013, Nature Genetics.

[13]  K. Ovaska,et al.  FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells. , 2013, Cancer research.

[14]  Inkyung Jung,et al.  Genetic Landscape of Open Chromatin in Yeast , 2013, PLoS genetics.

[15]  Kimberly D Siegmund,et al.  G9a functions as a molecular scaffold for assembly of transcriptional coactivators on a subset of Glucocorticoid Receptor target genes , 2012, Proceedings of the National Academy of Sciences.

[16]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[17]  A. Hecht,et al.  Intrinsic properties of Tcf1 and Tcf4 splice variants determine cell-type-specific Wnt/β-catenin target gene expression , 2012, Nucleic acids research.

[18]  Sonia Shah,et al.  Use of Allele-Specific FAIRE to Determine Functional Regulatory Polymorphism Using Large-Scale Genotyping Arrays , 2012, PLoS genetics.

[19]  B. Nadel,et al.  TLX homeodomain oncogenes mediate T cell maturation arrest in T-ALL via interaction with ETS1 and suppression of TCRα gene expression. , 2012, Cancer cell.

[20]  J. De-Castro Arce,et al.  Silencing of multi-copy HPV16 by viral self-methylation and chromatin occlusion: a model for epigenetic virus-host interaction. , 2012, Human molecular genetics.

[21]  Lukas Burger,et al.  Target genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin state , 2012, Proceedings of the National Academy of Sciences.

[22]  S. Keleş,et al.  Distal enhancers upstream of the Charcot-Marie-Tooth type 1A disease gene PMP22. , 2012, Human molecular genetics.

[23]  I. Tomlinson,et al.  Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression , 2012, Nature Genetics.

[24]  J. Lieb,et al.  Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription. , 2012, Genome research.

[25]  Dustin E. Schones,et al.  The Chromatin-binding Protein HMGN1 Regulates the Expression of Methyl CpG-binding Protein 2 (MECP2) and Affects the Behavior of Mice* , 2011, The Journal of Biological Chemistry.

[26]  Nathan C. Sheffield,et al.  Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. , 2011, Genome research.

[27]  H. Aburatani,et al.  Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation , 2011, PLoS genetics.

[28]  M. Lazar,et al.  Repressor transcription factor 7-like 1 promotes adipogenic competency in precursor cells , 2011, Proceedings of the National Academy of Sciences.

[29]  Peter J. Bickel,et al.  Measuring reproducibility of high-throughput experiments , 2011, 1110.4705.

[30]  P. Wolters,et al.  Interleukin-1β Induces Increased Transcriptional Activation of the Transforming Growth Factor-β-activating Integrin Subunit β8 through Altering Chromatin Architecture* , 2011, The Journal of Biological Chemistry.

[31]  J. Bähler,et al.  Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast , 2011, Genome Biology.

[32]  J. Stamatoyannopoulos,et al.  DNA methylation status predicts cell type‐specific enhancer activity , 2011, The EMBO journal.

[33]  M. Gut,et al.  Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters , 2011, Nature Structural &Molecular Biology.

[34]  J. Ibrahim,et al.  ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions , 2011, Genome Biology.

[35]  W. Mandemakers,et al.  Functional Dissection of the Oct6 Schwann Cell Enhancer Reveals an Essential Role for Dimeric Sox10 Binding , 2011, The Journal of Neuroscience.

[36]  Berthold Göttgens,et al.  Maps of Open Chromatin Guide the Functional Follow-Up of Genome-Wide Association Signals: Application to Hematological Traits , 2011, PLoS genetics.

[37]  Frederik Sommer,et al.  Transcription Factor–Dependent Chromatin Remodeling at Heat Shock and Copper-Responsive Promoters in Chlamydomonas reinhardtii[W][OA] , 2011, Plant Cell.

[38]  R. Nagarajan,et al.  Regulation of the PMP22 Gene through an Intronic Enhancer , 2011, The Journal of Neuroscience.

[39]  E. Birney,et al.  High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. , 2011, Genome research.

[40]  H. S. Kang,et al.  Retinoic acid-related orphan receptor γ directly regulates neuronal PAS domain protein 2 transcription in vivo , 2011, Nucleic acids research.

[41]  J. Carroll,et al.  FOXA1 is a critical determinant of Estrogen Receptor function and endocrine response , 2010, Nature Genetics.

[42]  Peter J. Park,et al.  An assessment of histone-modification antibody quality , 2010, Nature Structural &Molecular Biology.

[43]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[44]  E. Birney,et al.  Allele-specific and heritable chromatin signatures in humans. , 2010, Human molecular genetics.

[45]  Guillaume J. Filion,et al.  Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells , 2010, Cell.

[46]  Peter Saffrey,et al.  Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution , 2010, PloS one.

[47]  J. Ragoussis,et al.  Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. , 2010, Immunity.

[48]  G. Tuteja,et al.  Cell-Specific Determinants of Peroxisome Proliferator-Activated Receptor γ Function in Adipocytes and Macrophages , 2010, Molecular and Cellular Biology.

[49]  Shane C. Dillon,et al.  Genomic Approaches Uncover Increasing Complexities in the Regulatory Landscape at the Human SCL (TAL1) Locus , 2010, PloS one.

[50]  G. Crawford,et al.  DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. , 2010, Cold Spring Harbor protocols.

[51]  Kyle J. Gaulton,et al.  A map of open chromatin in human pancreatic islets , 2010, Nature Genetics.

[52]  F. Iborra,et al.  GFI1B controls its own expression binding to multiple sites , 2010, Haematologica.

[53]  Luke E. Berchowitz,et al.  A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae. , 2009, Genome research.

[54]  Carsten O. Daub,et al.  TagDust—a program to eliminate artifacts from next generation sequencing data , 2009, Bioinform..

[55]  R. Métivier,et al.  Functional Connection between Deimination and Deacetylation of Histones , 2009, Molecular and Cellular Biology.

[56]  P. Giresi,et al.  Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). , 2009, Methods.

[57]  Wei Sun,et al.  Improved ChIP-chip analysis by a mixture model approach , 2009, BMC Bioinformatics.

[58]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[59]  W. de Laat,et al.  Tissue- and Expression Level–Specific Chromatin Looping at Maize b1 Epialleles[W] , 2009, The Plant Cell Online.

[60]  Clifford A. Meyer,et al.  Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. , 2008, Genome research.

[61]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[62]  Terrence S. Furey,et al.  F-Seq: a feature density estimator for high-throughput sequence tags , 2008, Bioinform..

[63]  C. Paulus,et al.  Temporal Dynamics of Cytomegalovirus Chromatin Assembly in Productively Infected Human Cells , 2008, Journal of Virology.

[64]  Thomas D. Schmittgen,et al.  Analyzing real-time PCR data by the comparative CT method , 2008, Nature Protocols.

[65]  Mahesh Yaragatti,et al.  Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions. , 2008, Genome research.

[66]  Z. Weng,et al.  High-Resolution Mapping and Characterization of Open Chromatin across the Genome , 2008, Cell.

[67]  V. Iyer,et al.  FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. , 2007, Genome research.

[68]  Elena M Kramer,et al.  Virus-induced gene silencing as a tool for functional analyses in the emerging model plant Aquilegia (columbine, Ranunculaceae) , 2007, Plant Methods.

[69]  Andrew B Nobel,et al.  RNA chaperone activity and RNA-binding properties of the E. coli protein StpA , 2007, Nucleic acids research.

[70]  J. Lieb,et al.  Cell Cycle–Specified Fluctuation of Nucleosome Occupancy at Gene Promoters , 2006, PLoS genetics.

[71]  Richard A Young,et al.  Chromatin immunoprecipitation and microarray-based analysis of protein location , 2006, Nature Protocols.

[72]  M. Daly,et al.  Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). , 2005, Genome research.

[73]  J. Lieb,et al.  ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. , 2004, Genomics.

[74]  Patrick O. Brown,et al.  Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[75]  M. Groudine,et al.  Controlling the double helix , 2003, Nature.

[76]  J. D. Engel,et al.  A 200 base pair region at the 5′ end of the chicken adult β-globin gene is accessible to nuclease digestion , 1981, Cell.

[77]  J. D. Engel,et al.  Tissue-specific DNA cleavages in the globin chromatin domain introduced by DNAase I , 1980, Cell.

[78]  S. Rodríguez-Seguí,et al.  Mapping open chromatin with formaldehyde-assisted isolation of regulatory elements. , 2011, Methods in molecular biology.

[79]  M. Huss,et al.  Supplementary information for Integrative model of genomic factors for determining binding site selection by estrogen receptor α , 2010 .

[80]  S. Lonardi,et al.  Supplemental Material to : Nucleosome landscape and control of transcription in the human malaria parasite , 2009 .

[81]  Stuart L Schreiber,et al.  The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. , 2004, Methods in enzymology.

[82]  M. Oettinger,et al.  Chromatin immunoprecipitation in the analysis of large chromatin domains across murine antigen receptor loci. , 2004, Methods in enzymology.

[83]  Patrick Yau,et al.  High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. , 2004, Methods in enzymology.

[84]  Andrew J. Bannister,et al.  Histone methylation: recognizing the methyl mark. , 2004, Methods in enzymology.

[85]  K. Zaret,et al.  Sequential chromatin immunoprecipitation from animal tissues. , 2004, Methods in enzymology.

[86]  Bing Ren,et al.  Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. , 2004, Methods in enzymology.

[87]  J. Lieb,et al.  Genome-wide mapping of protein-DNA interactions by chromatin immunoprecipitation and DNA microarray hybridization. , 2003, Methods in molecular biology.

[88]  M. Oberley,et al.  Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. , 2003, Methods in enzymology.

[89]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[90]  D. S. Gross,et al.  Nuclease hypersensitive sites in chromatin. , 1988, Annual review of biochemistry.

[91]  S. Elgin,et al.  DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[92]  Heng Li,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .