Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome

[1]  Fredrick R. Schumacher,et al.  Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry , 2016, Nature Genetics.

[2]  Roland Eils,et al.  Active medulloblastoma enhancers reveal subgroup-specific cellular origins , 2016, Nature.

[3]  Marcin Imielinski,et al.  Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers , 2015, Nature Genetics.

[4]  James E. Bradner,et al.  Response and resistance to BET bromodomain inhibitors in triple negative breast cancer , 2015, Nature.

[5]  A. Butte,et al.  Systematic pan-cancer analysis of tumour purity , 2015, Nature Communications.

[6]  D. Durocher,et al.  High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities , 2015, Cell.

[7]  W. Pear,et al.  Tribbles in normal and malignant haematopoiesis , 2015, Biochemical Society transactions.

[8]  A. Carracedo,et al.  Oncosuppressive functions of tribbles pseudokinase 3. , 2015, Biochemical Society transactions.

[9]  P. Zhao,et al.  Downregulated expression of PHLDA1 protein is associated with a malignant phenotype of cholangiocarcinoma. , 2015, Oncology letters.

[10]  S. Spicuglia.  Faculty Opinions recommendation of Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. , 2015 .

[11]  P. Labhart,et al.  Context-specific role of SOX9 in NF-Y mediated gene regulation in colorectal cancer cells , 2015, Nucleic acids research.

[12]  P. Zhao,et al.  Correlation of decreased expression of PHLDA1 protein with malignant phenotype of gastric adenocarcinoma. , 2015, International journal of clinical and experimental pathology.

[13]  Lei Zhou,et al.  Common genetic variant on BMP4 contributes to colorectal adenoma and cancer: A meta-analysis based on 15 studies. , 2015, Cytokine.

[14]  Charles Y. Lin,et al.  Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. , 2015, Molecular cell.

[15]  Boris Lenhard,et al.  Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin , 2015 .

[16]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[17]  J. Stender,et al.  Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities , 2015, Cell.

[18]  Yijun Ruan,et al.  B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity , 2014, Cell.

[19]  James E. Bradner,et al.  Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability , 2014, Cell.

[20]  J. Stender,et al.  Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities , 2014, Cell.

[21]  R. Young,et al.  An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element , 2014, Science.

[22]  Peggy J. Farnham,et al.  Functional annotation of colon cancer risk SNPs , 2014, Nature Communications.

[23]  Emmanouil T. Dermitzakis,et al.  Putative cis-regulatory drivers in colorectal cancer , 2014, Nature.

[24]  Daniel C. Factor,et al.  Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency. , 2014, Cell stem cell.

[25]  Jahn M. Nesland,et al.  Prognostic Significance of β-Catenin, E-Cadherin, and SOX9 in Colorectal Cancer: Results from a Large Population-Representative Series , 2014, Front. Oncol..

[26]  Yan Guo,et al.  Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk , 2014, Nature Genetics.

[27]  Tao Xi,et al.  miR-155 regulates the proliferation and cell cycle of colorectal carcinoma cells by targeting E2F2 , 2014, Biotechnology Letters.

[28]  J. Beaulieu,et al.  Modulation of stemness in a human normal intestinal epithelial crypt cell line by activation of the WNT signaling pathway. , 2014, Experimental cell research.

[29]  C. Carlson,et al.  Genome-Wide Diet-Gene Interaction Analyses for Risk of Colorectal Cancer , 2014, PLoS genetics.

[30]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[31]  M. Lupien,et al.  Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits , 2014, Genome research.

[32]  J. Lieb,et al.  What are super-enhancers? , 2014, Nature Genetics.

[33]  Charles Y. Lin,et al.  Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma. , 2013, Cancer cell.

[34]  Boris Lenhard,et al.  Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments , 2013, Genome research.

[35]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[36]  Richard M Myers,et al.  Mapping genome-wide transcription factor binding sites in frozen tissues , 2013, Epigenetics & Chromatin.

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

[38]  M. Vinciguerra,et al.  Interplay between SOX9, β-catenin and PPARγ activation in colorectal cancer. , 2013, Biochimica et biophysica acta.

[39]  Jeffrey J Meyer,et al.  Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012. (5) , 2013 .

[40]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[41]  David A. Orlando,et al.  Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers , 2013, Cell.

[42]  Bradley E. Bernstein,et al.  Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues , 2013, Cell.

[43]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[44]  A. Regev,et al.  The Histone Deacetylase SIRT6 Is a Tumor Suppressor that Controls Cancer Metabolism , 2012, Cell.

[45]  H. Varmus,et al.  Sensitivity of human lung adenocarcinoma cell lines to targeted inhibition of BET epigenetic signaling proteins , 2012, Proceedings of the National Academy of Sciences.

[46]  I. Yeh,et al.  Differential expression of PHLDA1 (TDAG51) in basal cell carcinoma and trichoepithelioma , 2012, The British journal of dermatology.

[47]  Swneke D. Bailey,et al.  Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression , 2012, Nature Genetics.

[48]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of human colon and rectal cancer , 2012, Nature.

[49]  Jason H. Moore,et al.  Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer , 2012, Science.

[50]  S. Robson,et al.  Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia , 2011, Nature.

[51]  P. Sandy,et al.  Targeting MYC dependence in cancer by inhibiting BET bromodomains , 2011, Proceedings of the National Academy of Sciences.

[52]  R. Young,et al.  BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc , 2011, Cell.

[53]  P. Scacheri,et al.  Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. , 2011, Genome research.

[54]  Jaak Vilo,et al.  g:Profiler—a web server for functional interpretation of gene lists (2011 update) , 2011, Nucleic Acids Res..

[55]  Steven Gallinger,et al.  Multiple Common Susceptibility Variants near BMP Pathway Loci GREM1, BMP4, and BMP2 Explain Part of the Missing Heritability of Colorectal Cancer , 2011, PLoS genetics.

[56]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[57]  Nathan Brown,et al.  Evaluation of Germline BMP4 Mutation as a Cause of Colorectal Cancer , 2011, Human mutation.

[58]  Gary D Bader,et al.  Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.

[59]  William B. Smith,et al.  Selective inhibition of BET bromodomains , 2010, Nature.

[60]  Miguel Manzanares,et al.  Allelic Variation at the 8q23.3 Colorectal Cancer Risk Locus Functions as a Cis-Acting Regulator of EIF3H , 2010, PLoS genetics.

[61]  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.

[62]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[63]  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 .

[64]  Kaoru Tanaka,et al.  FOXQ1 is overexpressed in colorectal cancer and enhances tumorigenicity and tumor growth. , 2010, Cancer research.

[65]  M. McArthur,et al.  E2F2 suppresses Myc‐induced proliferation and tumorigenesis , 2010, Molecular carcinogenesis.

[66]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[67]  I. Ial,et al.  Nature Communications , 2010, Nature Cell Biology.

[68]  M. Bertagnolli,et al.  Molecular origins of cancer: Molecular basis of colorectal cancer. , 2009, The New England journal of medicine.

[69]  Michael D. Wilson,et al.  ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. , 2009, Methods.

[70]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[71]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[72]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

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

[74]  Steven Gallinger,et al.  Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer , 2008, Nature Genetics.

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

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

[77]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[78]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[79]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[80]  A. Sparks,et al.  Identification of c-MYC as a target of the APC pathway. , 1998, Science.

[81]  B. Vogelstein,et al.  A genetic model for colorectal tumorigenesis , 1990, Cell.

[82]  J. Willson,et al.  Cell culture of human colon adenomas and carcinomas. , 1987, Cancer research.