Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

[1]  Judith B. Zaugg,et al.  Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions , 2015, Cell.

[2]  Eli J. Fine,et al.  DNA targeting specificity of RNA-guided Cas9 nucleases , 2013, Nature Biotechnology.

[3]  Annette Lee,et al.  Genome-wide association study in alopecia areata implicates both innate and adaptive immunity , 2010, Nature.

[4]  Hailiang Huang,et al.  Fine-mapping inflammatory bowel disease loci to single variant resolution , 2017, Nature.

[5]  Thomas M. Norman,et al.  A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response , 2016, Cell.

[6]  I. Weissman,et al.  Index switching causes “spreading-of-signal” among multiplexed samples in Illumina HiSeq 4000 DNA sequencing , 2017, bioRxiv.

[7]  E. Lander,et al.  Local regulation of gene expression by lncRNA promoters, transcription and splicing , 2016, Nature.

[8]  Tom Michoel,et al.  Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases , 2016, Science.

[9]  Manolis Kellis,et al.  Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers , 2015, Nature Genetics.

[10]  Riitta Lahesmaa,et al.  Genomic views of STAT function in CD4+ T helper cell differentiation , 2011, Nature Reviews Immunology.

[11]  Daphne Koller,et al.  Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes , 2014, Science.

[12]  Manolis Kellis,et al.  Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease , 2015, Nature.

[13]  J. Danesh,et al.  Large-scale association analysis identifies new risk loci for coronary artery disease , 2013 .

[14]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[15]  Michael Q. Zhang,et al.  Integrative analysis of haplotype-resolved epigenomes across human tissues , 2015, Nature.

[16]  Clint L. Miller,et al.  Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells That Contribute to the Fibrous Cap , 2015, PLoS genetics.

[17]  Neville E. Sanjana,et al.  High-resolution interrogation of functional elements in the noncoding genome , 2016, Science.

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

[19]  Philip A. Ewels,et al.  Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C , 2015, Nature Genetics.

[20]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

[21]  Jonathan C. Cohen,et al.  A Common Allele on Chromosome 9 Associated with Coronary Heart Disease , 2007, Science.

[22]  A. Dunning,et al.  Beyond GWASs: illuminating the dark road from association to function. , 2013, American journal of human genetics.

[23]  Jing Liang,et al.  Chromatin architecture reorganization during stem cell differentiation , 2015, Nature.

[24]  Shane J. Neph,et al.  A comparative encyclopedia of DNA elements in the mouse genome , 2014, Nature.

[25]  Howard Y. Chang,et al.  HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.

[26]  H. Weiner,et al.  Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells , 2006, Nature.

[27]  D. Jarrossay,et al.  Surface phenotype and antigenic specificity of human interleukin 17–producing T helper memory cells , 2007, Nature Immunology.

[28]  G. Plitas,et al.  Genetic and epigenetic variation in the lineage specification of regulatory T cells , 2015, eLife.

[29]  Howard Y. Chang,et al.  Discovery of stimulation-responsive immune enhancers with CRISPR activation , 2017, Nature.

[30]  Jonathan M. Cairns,et al.  Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters , 2016, Cell.

[31]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

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

[33]  Max A. Horlbeck,et al.  Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation , 2014, Cell.

[34]  Lan T M Dao,et al.  Genome-wide characterization of mammalian promoters with distal enhancer functions , 2017, Nature Genetics.

[35]  Raymond K. Auerbach,et al.  Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.

[36]  R. Collins,et al.  Genetic variants associated with Lp(a) lipoprotein level and coronary disease. , 2009, The New England journal of medicine.

[37]  Yasmine Belkaid,et al.  The Alarmin IL-33 Promotes Regulatory T Cell Function in the Intestine , 2014, Nature.

[38]  H. Bussemaker,et al.  In search of the determinants of enhancer-promoter interaction specificity. , 2014, Trends in cell biology.

[39]  Sharon R Grossman,et al.  Systematic mapping of functional enhancer–promoter connections with CRISPR interference , 2016, Science.

[40]  Meagan E. Sullender,et al.  Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 , 2015, Nature Biotechnology.

[41]  R. Young,et al.  Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.

[42]  A. Gylfason,et al.  A Common Variant on Chromosome 9p21 Affects the Risk of Myocardial Infarction , 2007, Science.

[43]  Jingyuan Fu,et al.  Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression , 2013, PLoS genetics.

[44]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[45]  Max A. Horlbeck,et al.  Nucleosomes impede Cas9 access to DNA in vivo and in vitro , 2016, eLife.

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

[47]  V. Ranzani,et al.  De novo transcriptome profiling of highly purified human lymphocytes primary cells , 2015, Scientific Data.

[48]  Max A. Horlbeck,et al.  Nucleosomes Impede Cas 9 Access to DNA in vivo and in vitro , 2016 .

[49]  Chun Jimmie Ye,et al.  Intersection of population variation and autoimmunity genetics in human T cell activation , 2014, Science.

[50]  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.

[51]  N. Cox,et al.  Obesity-associated variants within FTO form long-range functional connections with IRX3 , 2014, Nature.

[52]  M. Daly,et al.  Genetic and Epigenetic Fine-Mapping of Causal Autoimmune Disease Variants , 2014, Nature.

[53]  B. Stranger,et al.  Interindividual variation in human T regulatory cells , 2014, Proceedings of the National Academy of Sciences.

[54]  Trieu Nguyen,et al.  Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci , 2016, Nature Communications.

[55]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[56]  Manolis Kellis,et al.  ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.

[57]  Manolis Kellis,et al.  FTO Obesity Variant Circuitry and Adipocyte Browning in Humans. , 2015, The New England journal of medicine.

[58]  H. Ueno,et al.  Human blood CXCR5(+)CD4(+) T cells are counterparts of T follicular cells and contain specific subsets that differentially support antibody secretion. , 2011, Immunity.

[59]  M. Daly,et al.  Genetic Mapping in Human Disease , 2008, Science.

[60]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[61]  Shane J. Neph,et al.  Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification , 2012, Cell.