Bridging epigenomics and complex disease: the basics

[1]  Caspar Zialor.  DNA sequencing with chain terminating inhibitors , 2014 .

[2]  David G. Knowles,et al.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.

[3]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[4]  Lee E. Edsall,et al.  A map of the cis-regulatory sequences in the mouse genome , 2012, Nature.

[5]  Howard Cedar,et al.  Programming of DNA methylation patterns. , 2012, Annual review of biochemistry.

[6]  Chris Sander,et al.  A Role for Neuronal piRNAs in the Epigenetic Control of Memory-Related Synaptic Plasticity , 2012, Cell.

[7]  M. Esteller,et al.  Cancer epigenomics: beyond genomics. , 2012, Current opinion in genetics & development.

[8]  Jonathan M. Mudge,et al.  Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells , 2012, PloS one.

[9]  Thomas Lengauer,et al.  Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types , 2011, PLoS genetics.

[10]  Howard Y. Chang,et al.  Molecular mechanisms of long noncoding RNAs. , 2011, Molecular cell.

[11]  Zhike Lu,et al.  Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification , 2011, Cell.

[12]  R. DeFronzo,et al.  Chromatin occupancy of transcription factor 7-like 2 (TCF7L2) and its role in hepatic glucose metabolism , 2011, Diabetologia.

[13]  J. Rinn,et al.  lincRNAs act in the circuitry controlling pluripotency and differentiation , 2011, Nature.

[14]  D. Balding,et al.  Epigenome-wide association studies for common human diseases , 2011, Nature Reviews Genetics.

[15]  P. Fraser,et al.  No-Nonsense Functions for Long Noncoding RNAs , 2011, Cell.

[16]  Tao Liu,et al.  A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism , 2011, Science.

[17]  Timothy J. Durham,et al.  "Systematic" , 1966, Comput. J..

[18]  A. Bird,et al.  Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability , 2011, Nature.

[19]  J. Einasto.  Dark Matter , 2011, Brazilian Journal of Physics.

[20]  S. Beck,et al.  Cancer epigenome. , 2010, Advances in genetics.

[21]  Zhiping Weng,et al.  Paternally Induced Transgenerational Environmental Reprogramming of Metabolic Gene Expression in Mammals , 2010, Cell.

[22]  G. Mack.  To selectivity and beyond , 2010, Nature Biotechnology.

[23]  Margaret J. Morris,et al.  Chronic high-fat diet in fathers programs β-cell dysfunction in female rat offspring , 2010, Nature.

[24]  A. Kasarskis,et al.  A window into third-generation sequencing. , 2010, Human molecular genetics.

[25]  Eric S. Lander,et al.  Comparative Epigenomic Analysis of Murine and Human Adipogenesis , 2010, Cell.

[26]  Robert B Darnell,et al.  HITS‐CLIP: panoramic views of protein–RNA regulation in living cells , 2010, Wiley interdisciplinary reviews. RNA.

[27]  Michael Q. Zhang,et al.  Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications , 2010, Nature Biotechnology.

[28]  Yi Zhang,et al.  Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification , 2010, Nature.

[29]  J. Ule,et al.  iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution , 2010, Nature Structural &Molecular Biology.

[30]  Manolis Kellis,et al.  Discovery and characterization of chromatin states for systematic annotation of the human genome , 2010, Nature Biotechnology.

[31]  Arturas Petronis,et al.  Epigenetics as a unifying principle in the aetiology of complex traits and diseases , 2010, Nature.

[32]  T. Hughes,et al.  Most “Dark Matter” Transcripts Are Associated With Known Genes , 2010, PLoS biology.

[33]  David J Munroe,et al.  Third-generation sequencing fireworks at Marco Island , 2010, Nature Biotechnology.

[34]  Scott B. Dewell,et al.  Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.

[35]  Helen M. Blau,et al.  Reprogramming towards pluripotency requires AID-dependent DNA demethylation , 2010, Nature.

[36]  Yixue Li,et al.  Regulation of Cellular Metabolism by Protein Lysine Acetylation , 2010, Science.

[37]  A. Feinberg,et al.  Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease , 2010, Proceedings of the National Academy of Sciences.

[38]  David Serre,et al.  MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome , 2009, Nucleic acids research.

[39]  Nir Friedman,et al.  High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. , 2010, Genome research.

[40]  M. Esteller,et al.  DNA methylation and cancer. , 2010, Advances in genetics.

[41]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[42]  Daniel F. Gudbjartsson,et al.  Parental origin of sequence variants associated with complex diseases , 2009, Nature.

[43]  L. Groop,et al.  Epigenetics: A Molecular Link Between Environmental Factors and Type 2 Diabetes , 2009, Diabetes.

[44]  Lee E. Edsall,et al.  Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.

[45]  H. Putter,et al.  DNA methylation differences after exposure to prenatal famine are common and timing- and sex-specific. , 2009, Human molecular genetics.

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

[47]  D. Reinberg,et al.  Calorie restriction and the exercise of chromatin. , 2009, Genes & development.

[48]  M. Mann,et al.  Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions , 2009, Science.

[49]  B. Richardson,et al.  The genetics and epigenetics of autoimmune diseases. , 2009, Journal of autoimmunity.

[50]  Y. Ruan,et al.  ChIP‐based methods for the identification of long‐range chromatin interactions , 2009, Journal of cellular biochemistry.

[51]  Yi Zhang,et al.  Role of Jhdm2a in regulating metabolic gene expression and obesity resistance , 2009, Nature.

[52]  Gene W. Yeo,et al.  An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells , 2009, Nature Structural &Molecular Biology.

[53]  M. Cooper,et al.  Hyperglycemia Induces a Dynamic Cooperativity of Histone Methylase and Demethylase Enzymes Associated With Gene-Activating Epigenetic Marks That Coexist on the Lysine Tail , 2008, Diabetes.

[54]  E. Olson,et al.  The many roles of histone deacetylases in development and physiology: implications for disease and therapy , 2009, Nature Reviews Genetics.

[55]  R. Sachidanandam,et al.  An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing , 2008, Science.

[56]  R. Roeder,et al.  Transient high glucose causes persistent epigenetic changes and altered gene expression during subsequent normoglycemia , 2008, The Journal of Experimental Medicine.

[57]  R. Durbin,et al.  A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis , 2008, Nature Biotechnology.

[58]  G. Hannon,et al.  The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race , 2007, Science.

[59]  Peter Fraser,et al.  Gene regulation through nuclear organization , 2007, Nature Structural &Molecular Biology.

[60]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[61]  J. Auwerx,et al.  Transcriptional coregulators in the control of energy homeostasis. , 2007, Trends in cell biology.

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

[63]  A. Feinberg.  Phenotypic plasticity and the epigenetics of human disease , 2007, Nature.

[64]  J. Mattick.  A new paradigm for developmental biology , 2007, Journal of Experimental Biology.

[65]  H. Scott,et al.  Modifiers of epigenetic reprogramming show paternal effects in the mouse , 2007, Nature Genetics.

[66]  R. Jirtle,et al.  Environmental epigenomics and disease susceptibility , 2007, Nature Reviews Genetics.

[67]  K. Sandhu,et al.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions , 2006, Nature Genetics.

[68]  N. C. Schanen,et al.  Epigenetics of autism spectrum disorders. , 2006, Human molecular genetics.

[69]  C. Nusbaum,et al.  Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. , 2006, Genome research.

[70]  Yvonne Tay,et al.  A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes , 2006, Cell.

[71]  Liang-Hu Qu,et al.  snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome , 2006, Nucleic acids research.

[72]  N. Grishin,et al.  Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. , 2006, Molecular cell.

[73]  C. Glass,et al.  Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response. , 2006, Genes & development.

[74]  H. Stefánsson,et al.  Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes , 2006, Nature Genetics.

[75]  S. Stamm,et al.  The snoRNA HBII-52 Regulates Alternative Splicing of the Serotonin Receptor 2C , 2006, Science.

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

[77]  A. Gnirke,et al.  Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis , 2005, Nucleic acids research.

[78]  T. Spector,et al.  Epigenetic differences arise during the lifetime of monozygotic twins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[79]  J. Mendell.  MicroRNAs: Critical Regulators of Development, Cellular Physiology and Malignancy , 2005, Cell cycle.

[80]  W. Lam,et al.  Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells , 2005, Nature Genetics.

[81]  Si-guang Li,et al.  Identification and Functional Analysis of 20 Box H/ACA Small Nucleolar RNAs (snoRNAs) from Schizosaccharomyces pombe* , 2005, Journal of Biological Chemistry.

[82]  Steven P Gygi,et al.  Nutrient control of glucose homeostasis through a complex of PGC-1alpha and SIRT1. , 2005, Nature.

[83]  Bruce M. Spiegelman,et al.  Biological Control through Regulated Transcriptional Coactivators , 2004, Cell.

[84]  Michael J Meaney,et al.  Epigenetic programming by maternal behavior , 2004, Nature Neuroscience.

[85]  Bert W O'Malley,et al.  Coregulator function: a key to understanding tissue specificity of selective receptor modulators. , 2004, Endocrine reviews.

[86]  Jernej Ule,et al.  CLIP Identifies Nova-Regulated RNA Networks in the Brain , 2003, Science.

[87]  M. Fournier,et al.  Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. , 2003, Molecular cell.

[88]  J. Bach,et al.  The effect of infections on susceptibility to autoimmune and allergic diseases. , 2002, The New England journal of medicine.

[89]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[90]  S. Niranjanakumari,et al.  Reversible cross-linking combined with immunoprecipitation to study RNA-protein interactions in vivo. , 2002, Methods.

[91]  M. Krstic-Demonacos,et al.  Acetylation control of the retinoblastoma tumour-suppressor protein , 2001, Nature Cell Biology.

[92]  Haifan Lin,et al.  Yb modulates the divisions of both germline and somatic stem cells through piwi- and hh-mediated mechanisms in the Drosophila ovary. , 2001, Molecular cell.

[93]  N. Mahmud,et al.  Human CD34(+) stem cells express the hiwi gene, a human homologue of the Drosophila gene piwi. , 2001, Blood.

[94]  A. Bird,et al.  Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

[96]  David I. K. Martin,et al.  Epigenetic inheritance at the agouti locus in the mouse , 1999, Nature Genetics.

[97]  P. O'Connell,et al.  Linkage of type 2 diabetes mellitus and of age at onset to a genetic location on chromosome 10q in Mexican Americans. , 1999, American journal of human genetics.

[98]  J. Steitz,et al.  Modification of U6 spliceosomal RNA is guided by other small RNAs. , 1998, Molecular cell.

[99]  Wei Gu,et al.  Activation of p53 Sequence-Specific DNA Binding by Acetylation of the p53 C-Terminal Domain , 1997, Cell.

[100]  J. Ni,et al.  Small Nucleolar RNAs Direct Site-Specific Synthesis of Pseudouridine in Ribosomal RNA , 1997, Cell.

[101]  J. Herman,et al.  Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[102]  Tamás Kiss,et al.  Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs , 1996, Cell.

[103]  Rudolf Jaenisch,et al.  Role for DNA methylation in genomic imprinting , 1993, Nature.

[104]  H. Nielsen,et al.  A novel class of nucleolar RNAs from Tetrahymena , 1992, FEBS letters.

[105]  E. Raleigh,et al.  McrBC: a multisubunit GTP-dependent restriction endonuclease. , 1992, Journal of molecular biology.

[106]  L. E. McDonald,et al.  A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[107]  F. Sanger,et al.  A Rapid Method for Determining Sequences in DNA by Primed Synthesis with DNA Polymerase , 1989 .

[108]  Alexander Varshavsky,et al.  Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene , 1988, Cell.

[109]  A. Bird.  DNA methylation versus gene expression. , 1984, Journal of embryology and experimental morphology.

[110]  M. Szyf,et al.  DNA methylation patterns. Formation and function. , 1984, Biochimica et biophysica acta.

[111]  J. Lis,et al.  Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[112]  B. Migeon,et al.  Methylation of the hypoxanthine phosphoribosyltransferase locus on the human X chromosome: implications for X-chromosome inactivation. , 1984, Proceedings of the National Academy of Sciences of the United States of America.