Heterarchy of transcription factors driving basal and luminal cell phenotypes in human urothelium

[1]  G. Sauter,et al.  Diverse expression patterns of the EMT suppressor grainyhead‐like 2 (GRHL2) in normal and tumour tissues , 2016, International journal of cancer.

[2]  Neva C. Durand,et al.  Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes , 2015, Proceedings of the National Academy of Sciences.

[3]  M. Höglund,et al.  Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems , 2015, BMC Medical Genomics.

[4]  Kyle J. Gaulton,et al.  Lipid-Induced Epigenomic Changes in Human Macrophages Identify a Coronary Artery Disease-Associated Variant that Regulates PPAP2B Expression through Altered C/EBP-Beta Binding , 2015, PLoS genetics.

[5]  Y. Kluger,et al.  Comparative FAIRE‐seq Analysis Reveals Distinguishing Features of the Chromatin Structure of Ground State‐ and Primed‐Pluripotent Cells , 2015, Stem cells.

[6]  Jennifer Southgate,et al.  The human urothelial tight junction: claudin 3 and the ZO-1α+ switch , 2015, Bladder.

[7]  J. Eeckhoute,et al.  A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation , 2014, Nucleic acids research.

[8]  Juri Rappsilber,et al.  Chromatin enrichment for proteomics , 2014, Nature Protocols.

[9]  Xavier Paoletti,et al.  EGFR as a potential therapeutic target for a subset of muscle-invasive bladder cancers presenting a basal-like phenotype , 2014, Science Translational Medicine.

[10]  J. Southgate,et al.  Plasticity of in vitro-generated urothelial cells for functional tissue formation. , 2014, Tissue engineering. Part A.

[11]  S. Kramer,et al.  Identification of ELF3 as an early transcriptional regulator of human urothelium. , 2014, Developmental biology.

[12]  K. Baggerly,et al.  Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy. , 2014, Cancer cell.

[13]  J. Southgate,et al.  Plasticity of in vitro-generated urothelial cells for functional tissue formation. , 2014, Tissue engineering. Part A.

[14]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.

[15]  J. Southgate,et al.  Differential expression of Oct4 variants and pseudogenes in normal urothelium and urothelial cancer. , 2013, The American journal of pathology.

[16]  P. Lefevre,et al.  CTCF depletion alters chromatin structure and transcription of myeloid-specific factors. , 2013, Journal of molecular cell biology.

[17]  V. Theodorou,et al.  GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility , 2013, Genome research.

[18]  B. Czerniak,et al.  The p63 Protein Isoform ΔNp63α Inhibits Epithelial-Mesenchymal Transition in Human Bladder Cancer Cells , 2012, The Journal of Biological Chemistry.

[19]  C. Taylor,et al.  Novel Tumor Subgroups of Urothelial Carcinoma of the Bladder Defined by Integrated Genomic Analysis , 2012, Clinical Cancer Research.

[20]  Shahrokh F. Shariat,et al.  Loss of the Urothelial Differentiation Marker FOXA1 Is Associated with High Grade, Late Stage Bladder Cancer and Increased Tumor Proliferation , 2012, PloS one.

[21]  C. Dinney,et al.  p63 Expression Defines a Lethal Subset of Muscle-Invasive Bladder Cancers , 2012, PloS one.

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

[23]  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.

[24]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[25]  J. Whitsett,et al.  Kruppel-like factor 5 is required for formation and differentiation of the bladder urothelium. , 2011, Developmental biology.

[26]  Tao Liu,et al.  Using MACS to Identify Peaks from ChIP‐Seq Data , 2011, Current protocols in bioinformatics.

[27]  A. Sabichi,et al.  System level changes in gene expression in maturing bladder mucosa. , 2011, The Journal of urology.

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

[29]  Scott Lowe,et al.  Distinct expression profiles of p63 variants during urothelial development and bladder cancer progression. , 2011, The American journal of pathology.

[30]  N. Galjart,et al.  Functional analysis of CTCF during mammalian limb development. , 2010, Developmental cell.

[31]  Michael Bader,et al.  The transcription factor grainyhead-like 2 regulates the molecular composition of the epithelial apical junctional complex , 2010, Development.

[32]  G. Daley,et al.  All-Trans Retinoic Acid Directs Urothelial Specification of Murine Embryonic Stem Cells via GATA4/6 Signaling Mechanisms , 2010, PloS one.

[33]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[34]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

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

[36]  Karen L. Mohlke,et al.  A map of open chromatin in human pancreatic islets , 2010, Nature Genetics.

[37]  Zhengquan Yu,et al.  The epidermal differentiation‐associated Grainyhead gene Get1/Grhl3 also regulates urothelial differentiation , 2009, The EMBO journal.

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

[39]  Israel Steinfeld,et al.  BMC Bioinformatics BioMed Central , 2008 .

[40]  N. Galjart,et al.  CTCF regulates cell cycle progression of αβ T cells in the thymus , 2008, The EMBO journal.

[41]  N. D. Clarke,et al.  Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells , 2008, Cell.

[42]  U. Nagele,et al.  Immunoreactivity of p63 in monolayered and in vitro stratified human urothelial cell cultures compared with native urothelial tissue. , 2008, European urology.

[43]  Clifford A. Meyer,et al.  FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription , 2008, Cell.

[44]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

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

[46]  Robert J. Marinelli,et al.  Placental S100 (S100P) and GATA3: Markers for Transitional Epithelium and Urothelial Carcinoma Discovered by Complementary DNA Microarray , 2007, The American journal of surgical pathology.

[47]  Clifford A. Meyer,et al.  Genome-wide analysis of estrogen receptor binding sites , 2006, Nature Genetics.

[48]  J. Southgate,et al.  PPARγ‐regulated tight junction development during human urothelial cytodifferentiation , 2006, Journal of cellular physiology.

[49]  Jennifer Southgate,et al.  Autocrine regulation of human urothelial cell proliferation and migration during regenerative responses in vitro. , 2005, Experimental cell research.

[50]  J. Southgate,et al.  Activation of peroxisome proliferator-activated receptor-gamma reverses squamous metaplasia and induces transitional differentiation in normal human urothelial cells. , 2004, The American journal of pathology.

[51]  J. Southgate,et al.  Role of PPAR γ and EGFR signalling in the urothelial terminal differentiation programme , 2004, Journal of Cell Science.

[52]  G. Hall,et al.  Uroplakin gene expression in normal human tissues and locally advanced bladder cancer , 2003, The Journal of pathology.

[53]  Frank R. Lin,et al.  Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. , 2002, Molecular cell.

[54]  H. Vogel,et al.  p63 is a p53 homologue required for limb and epidermal morphogenesis , 1999, Nature.

[55]  G. Hall,et al.  Uroplakin gene expression by normal and neoplastic human urothelium. , 1998, The American journal of pathology.

[56]  Z. Wu,et al.  Conditional ectopic expression of C/EBP beta in NIH-3T3 cells induces PPAR gamma and stimulates adipogenesis. , 1995, Genes & development.

[57]  B. Spiegelman,et al.  Stimulation of adipogenesis in fibroblasts by PPARγ2, a lipid-activated transcription factor , 1994, Cell.

[58]  D. F. Thomas,et al.  Normal human urothelial cells in vitro: proliferation and induction of stratification. , 1994, Laboratory investigation; a journal of technical methods and pathology.

[59]  The Cancer Genome Atlas Research Network,et al.  Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.

[60]  J. Southgate,et al.  FOXA1 and IRF-1 intermediary transcriptional regulators of PPARγ-induced urothelial cytodifferentiation , 2009, Cell Death and Differentiation.

[61]  T. Sun,et al.  Uroplakins as markers of urothelial differentiation. , 1999, Advances in experimental medicine and biology.