Regional DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes

[1]  B. Ren,et al.  Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome , 2012, Cell.

[2]  E. Whitelaw,et al.  Understanding transgenerational epigenetic inheritance via the gametes in mammals , 2012, Nature Reviews Genetics.

[3]  Michael D. Wilson,et al.  Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages , 2012, Cell.

[4]  Vijay K. Tiwari,et al.  DNA-binding factors shape the mouse methylome at distal regulatory regions , 2011, Nature.

[5]  David I. K. Martin,et al.  Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. , 2011, Genome research.

[6]  T. Nakano,et al.  Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development. , 2011, Genome research.

[7]  R. Sandberg,et al.  CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing , 2011, Nature.

[8]  S. Bergmann,et al.  The evolution of gene expression levels in mammalian organs , 2011, Nature.

[9]  Jean-François Millau,et al.  CTCF, cohesin, and histone variants: connecting the genome. , 2011, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[10]  W. Richard McCombie,et al.  Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates , 2011, Cell.

[11]  Denis Thieffry,et al.  RSAT 2011: regulatory sequence analysis tools , 2011, Nucleic Acids Res..

[12]  J. Bell,et al.  A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues , 2011, PLoS genetics.

[13]  R. F. Luco,et al.  Epigenetics in Alternative Pre-mRNA Splicing , 2011, Cell.

[14]  R. Shoemaker,et al.  Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. , 2010, Genome research.

[15]  T. Hansen,et al.  Identification of KCNJ15 as a susceptibility gene in Asian patients with type 2 diabetes mellitus. , 2010, American journal of human genetics.

[16]  Martin J Aryee,et al.  Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts , 2009, Nature Genetics.

[17]  Michael Rehli,et al.  Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences. , 2009, Genome research.

[18]  V. Corces,et al.  CTCF: Master Weaver of the Genome , 2009, Cell.

[19]  J. Bohl,et al.  Differences in DNA methylation patterns and expression of the CCRK gene in human and nonhuman primate cortices. , 2009, Molecular biology and evolution.

[20]  Alicia Oshlack,et al.  Segmental Duplications Contribute to Gene Expression Differences Between Humans and Chimpanzees , 2009, Genetics.

[21]  E. Zwarthoff,et al.  Meningioma 1 Is Required for Appropriate Osteoblast Proliferation, Motility, Differentiation, and Function* , 2009, The Journal of Biological Chemistry.

[22]  K. Eckert,et al.  Every microsatellite is different: Intrinsic DNA features dictate mutagenesis of common microsatellites present in the human genome , 2009, Molecular carcinogenesis.

[23]  A. Feinberg,et al.  Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.

[24]  Rafael A. Irizarry,et al.  Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.

[25]  Alicia Oshlack,et al.  Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures , 2008, PLoS genetics.

[26]  E. Birney,et al.  An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). , 2008, Genome research.

[27]  T. Mikkelsen,et al.  Genome-scale DNA methylation maps of pluripotent and differentiated cells , 2008, Nature.

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

[29]  S. Cobb The facial skeleton of the chimpanzee‐human last common ancestor , 2008, Journal of anatomy.

[30]  G. Grosveld MN1, a novel player in human AML. , 2007, Blood cells, molecules & diseases.

[31]  Adrien E. Chabot,et al.  Using Reporter Gene Assays to Identify cis Regulatory Differences Between Humans and Chimpanzees , 2007, Genetics.

[32]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[33]  Michael Q. Zhang,et al.  Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome , 2007, Cell.

[34]  D. Cooper,et al.  Understanding the recent evolution of the human genome: insights from human–chimpanzee genome comparisons , 2007, Human mutation.

[35]  Y. Kashi,et al.  Simple sequence repeats as advantageous mutators in evolution. , 2006, Trends in genetics : TIG.

[36]  P. Pérez-Piñera,et al.  APP Processing and the APP-KPI Domain Involvement in the Amyloid Cascade , 2006, Neurodegenerative Diseases.

[37]  John K Field,et al.  Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[38]  S. Pääbo,et al.  Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees , 2005, Science.

[39]  S. Carroll,et al.  Evolution at Two Levels: On Genes and Form , 2005, PLoS biology.

[40]  P. Riegman,et al.  Targeted Disruption of the Mn1 Oncogene Results in Severe Defects in Development of Membranous Bones of the Cranial Skeleton , 2005, Molecular and Cellular Biology.

[41]  S. Chong,et al.  Epigenetic germline inheritance. , 2004, Current opinion in genetics & development.

[42]  E. Eichler,et al.  Regional patterns of gene expression in human and chimpanzee brains. , 2004, Genome research.

[43]  E. McConkey,et al.  Orthologous numbering of great ape and human chromosomes is essential for comparative genomics , 2004, Cytogenetic and Genome Research.

[44]  E. Nevo,et al.  Microsatellites within genes: structure, function, and evolution. , 2004, Molecular biology and evolution.

[45]  Wenbo Xu,et al.  Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[46]  P. Adorján,et al.  Differences in DNA methylation patterns between humans and chimpanzees , 2004, Current Biology.

[47]  Yoshiyuki Sakaki,et al.  A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. , 2004, Genome research.

[48]  Matthew A. Zapala,et al.  Elevated gene expression levels distinguish human from non-human primate brains , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[49]  J. Hacia,et al.  Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts. , 2003, Genome research.

[50]  Jacques van Helden,et al.  Regulatory Sequence Analysis Tools , 2003, Nucleic Acids Res..

[51]  C. Kanduri,et al.  The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains. , 2003, Genes & development.

[52]  G. Wray,et al.  Abundant raw material for cis-regulatory evolution in humans. , 2002, Molecular biology and evolution.

[53]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[54]  A. Camargo,et al.  Collagen XVIII, containing an endogenous inhibitor of angiogenesis and tumor growth, plays a critical role in the maintenance of retinal structure and in neural tube closure (Knobloch syndrome). , 2000, Human molecular genetics.

[55]  D. Haber,et al.  DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development , 1999, Cell.

[56]  C. Masters,et al.  The amyloid precursor protein of Alzheimer disease in human brain and blood , 1999, Journal of leukocyte biology.

[57]  B T Hyman,et al.  Neuropathology and apolipoprotein E profile of aged chimpanzees: implications for Alzheimer disease. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Rudolf Jaenisch,et al.  Targeted mutation of the DNA methyltransferase gene results in embryonic lethality , 1992, Cell.

[59]  J. Sawyer,et al.  The striking resemblance of high-resolution G-banded chromosomes of man and chimpanzee. , 1980, Science.

[60]  M. King,et al.  Evolution at two levels in humans and chimpanzees. , 1975, Science.

[61]  R. Britten,et al.  Gene regulation for higher cells: a theory. , 1969, Science.

[62]  T. Wisniewski,et al.  Molecular biology of Alzheimer's amyloid—Dutch variant , 2008, Molecular Neurobiology.

[63]  Gustavo Glusman,et al.  Initial sequence of the chimpanzee genome and comparison with the human genome , 2005 .

[64]  A. Bird DNA methylation patterns and epigenetic memory. , 2002, Genes & development.

[65]  J. Dumanski,et al.  Deregulation of the platelet-derived growth factor β-chain gene via fusion with collagen gene COL1A1 in dermatof ibrosarcoma protuberans and giant-cell fibroblastoma , 1997, Nature Genetics.

[66]  C. A. Thomas,et al.  Molecular cloning. , 1977, Advances in pathobiology.