Altered gene silencing and human diseases

Epigenetic regulation of gene expression is mediated through several mechanisms, including modifications in DNA methylation, covalent modifications of core nucleosomal histones, rearrangement of histones and RNA interference. It is now clear that deregulation of epigenetic mechanisms cooperates with genetic alterations in the development and progression of several Mendelian disorders. Here, we summarize the recent findings that highlight how certain inherited diseases, such as Rett syndrome, Immunodeficiency–centromeric instability–facial anomalies syndrome, and facioscapulohumeral muscular dystrophy, result from altered gene silencing.

[1]  R. Roeder,et al.  Transcriptional regulation and the role of diverse coactivators in animal cells , 2005, FEBS letters.

[2]  D. Bourc’his,et al.  Abnormal methylation does not prevent X inactivation in ICF patients , 1999, Cytogenetic and Genome Research.

[3]  C. Allis,et al.  Histone and chromatin cross-talk. , 2003, Current opinion in cell biology.

[4]  R. Jaenisch,et al.  Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[5]  B. Hendrich,et al.  MeCP2 in neurons: closing in on the causes of Rett syndrome. , 2005, Human molecular genetics.

[6]  N. Tommerup,et al.  Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene , 1999, Nature.

[7]  Giacomo Cavalli,et al.  Epigenetic inheritance of chromatin states mediated by Polycomb and trithorax group proteins in Drosophila. , 2005, Progress in molecular and subcellular biology.

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

[9]  D. Higgs,et al.  Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease , 2003, Nature Genetics.

[10]  T. Bestor,et al.  Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L , 2004, Nature.

[11]  R. Young,et al.  Transcription of eukaryotic protein-coding genes. , 2000, Annual review of genetics.

[12]  G. Lyons,et al.  The Polycomb Ezh2 methyltransferase regulates muscle gene expression and skeletal muscle differentiation. , 2004, Genes & development.

[13]  S. Riva,et al.  Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells. , 2005, Molecular biology of the cell.

[14]  A. Niveleau,et al.  Abnormal methylation pattern in constitutive and facultative (X inactive chromosome) heterochromatin of ICF patients. , 1994, Human molecular genetics.

[15]  J. Herman,et al.  Gene silencing in cancer in association with promoter hypermethylation. , 2003, The New England journal of medicine.

[16]  Noriyuki Kishi,et al.  MECP2 is progressively expressed in post-migratory neurons and is involved in neuronal maturation rather than cell fate decisions , 2004, Molecular and Cellular Neuroscience.

[17]  M. Robert,et al.  DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells , 2003, Nature Genetics.

[18]  R. Tupler,et al.  Molecular basis of facioscapulohumeral muscular dystrophy , 2004, Cellular and Molecular Life Sciences CMLS.

[19]  G. V. Ommen,et al.  Hypomethylation of D4Z4 in 4q-linked and non-4q-linked facioscapulohumeral muscular dystrophy , 2003, Nature Genetics.

[20]  Michael R Green,et al.  Eukaryotic transcription activation: right on target. , 2005, Molecular cell.

[21]  A. Bird,et al.  Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. , 1993, Nucleic acids research.

[22]  R. Eisenman,et al.  Histone sumoylation is associated with transcriptional repression , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[23]  S. Gygi,et al.  Two RNAi Complexes, RITS and RDRC, Physically Interact and Localize to Noncoding Centromeric RNAs , 2004, Cell.

[24]  C. Romano,et al.  Multibranched chromosomes 1, 9, and 16 in a patient with combined IgA and IgE deficiency , 1979, Human Genetics.

[25]  Daisuke Hattori,et al.  DNA Methylation-Related Chromatin Remodeling in Activity-Dependent Bdnf Gene Regulation , 2003, Science.

[26]  K. Robertson,et al.  The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors. , 1999, Nucleic acids research.

[27]  Edith Heard,et al.  Differential Histone H3 Lys-9 and Lys-27 Methylation Profiles on the X Chromosome , 2004, Molecular and Cellular Biology.

[28]  Tony Kouzarides,et al.  Acetylation: a regulatory modification to rival phosphorylation? , 2000, The EMBO journal.

[29]  James A. Birchler,et al.  Heterochromatic Silencing and HP1 Localization in Drosophila Are Dependent on the RNAi Machinery , 2004, Science.

[30]  M. Ares,et al.  The Spanish Connection Transcription and mRNA Processing Get Even Closer , 2005, Cell.

[31]  R. Hansen,et al.  X inactivation-specific methylation of LINE-1 elements by DNMT3B: implications for the Lyon repeat hypothesis. , 2003, Human molecular genetics.

[32]  Eric C. Griffith,et al.  Derepression of BDNF Transcription Involves Calcium-Dependent Phosphorylation of MeCP2 , 2003, Science.

[33]  Yi Zhang Transcriptional regulation by histone ubiquitination and deubiquitination. , 2003, Genes & development.

[34]  J. Strouboulis,et al.  Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription , 1998, Nature Genetics.

[35]  E. Li,et al.  Establishment and Maintenance of Genomic Methylation Patterns in Mouse Embryonic Stem Cells by Dnmt3a and Dnmt3b , 2003, Molecular and Cellular Biology.

[36]  C. Peterson,et al.  Histones and histone modifications , 2004, Current Biology.

[37]  M. Johnston,et al.  Developmental expression of methyl-CpG binding protein 2 is dynamically regulated in the rodent brain , 2004, Neuroscience.

[38]  J. Mellor,et al.  Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. , 2005, Molecular cell.

[39]  M. Hultén Selective Somatic Pairing and Fragility at 1q12 in a Boy with Common Variable Immuno Deficiency , 2008 .

[40]  M. Johnston,et al.  Neurobiology of Rett syndrome: a genetic disorder of synapse development , 2001, Brain and Development.

[41]  L. Lazzeroni,et al.  Gene expression patterns vary in clonal cell cultures from Rett syndrome females with eight different MECP2 mutations , 2002, BMC Medical Genetics.

[42]  R. Jaenisch,et al.  Induction of Tumors in Mice by Genomic Hypomethylation , 2003, Science.

[43]  J. Rubenstein,et al.  Developmental functions of the Distal-less/Dlx homeobox genes. , 2002, Development.

[44]  J E Hewitt,et al.  FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. , 1993, Human molecular genetics.

[45]  F. Brown,et al.  Stone Tools from Mid-Pleistocene Sediments in Java , 1978, Science.

[46]  A. Bird,et al.  MeCP2 Is a Transcriptional Repressor with Abundant Binding Sites in Genomic Chromatin , 1997, Cell.

[47]  H. Zoghbi,et al.  Insight into Rett syndrome: MeCP2 levels display tissue- and cell-specific differences and correlate with neuronal maturation. , 2002, Human molecular genetics.

[48]  Peter Cheung,et al.  Epigenetic regulation by histone methylation and histone variants. , 2005, Molecular endocrinology.

[49]  Jan-Fang Cheng,et al.  Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome , 2005, Nature Genetics.

[50]  Michael R. Green,et al.  Inappropriate Gene Activation in FSHD A Repressor Complex Binds a Chromosomal Repeat Deleted in Dystrophic Muscle , 2002, Cell.

[51]  M. Montecino,et al.  Poly(ADP-ribosylation) protects maternally derived histones from proteolysis after fertilization. , 1999, The Biochemical journal.

[52]  T. Bestor,et al.  Eukaryotic cytosine methyltransferases. , 2005, Annual review of biochemistry.

[53]  H. Horvitz,et al.  MicroRNA expression profiles classify human cancers , 2005, Nature.

[54]  R. Kuick,et al.  Whole-genome methylation scan in ICF syndrome: hypomethylation of non-satellite DNA repeats D4Z4 and NBL2. , 2000, Human molecular genetics.

[55]  V. Orlando,et al.  Epigenome programming by Polycomb and Trithorax proteins. , 2005, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[56]  Colin A. Johnson,et al.  Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex , 1998, Nature.

[57]  F. Ledeist,et al.  An embryonic-like methylation pattern of classical satellite DNA is observed in ICF syndrome. , 1993, Human molecular genetics.

[58]  E. Li Chromatin modification and epigenetic reprogramming in mammalian development , 2002, Nature Reviews Genetics.

[59]  D. Reinberg,et al.  Epigenetic Dynamics of Imprinted X Inactivation During Early Mouse Development , 2004, Science.

[60]  C. Wijmenga,et al.  The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[61]  A. Mégarbané,et al.  DNMT3B mutations and DNA methylation defect define two types of ICF syndrome , 2005, Human mutation.

[62]  S. Ishii,et al.  The Ski Protein Family Is Required for MeCP2-mediated Transcriptional Repression* , 2001, The Journal of Biological Chemistry.

[63]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[64]  Matthias Merkenschlager,et al.  Association of Transcriptionally Silent Genes with Ikaros Complexes at Centromeric Heterochromatin , 1997, Cell.

[65]  E. Seto,et al.  Regulation of histone deacetylase activities , 2004, Journal of cellular biochemistry.

[66]  M. Ehrlich,et al.  DNA hypomethylation and unusual chromosome instability in cell lines fromICF syndrome patients , 2000, Cytogenetic and Genome Research.

[67]  A. Fisher,et al.  Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. , 1999, Molecular cell.

[68]  S. Cross,et al.  CpG islands and genes. , 1995, Current opinion in genetics & development.

[69]  G. Miltenberger-Miltenyi,et al.  Mutations and polymorphisms in the human methyl CpG‐binding protein MECP2 , 2003, Human mutation.

[70]  K. Robertson,et al.  DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system. , 2004, Biochemical and biophysical research communications.

[71]  R. Feil,et al.  Epigenetic regulation of mammalian genomic imprinting. , 2004, Current opinion in genetics & development.

[72]  J. Birchler,et al.  RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. , 2002, Molecular cell.

[73]  Stefan Kubicek,et al.  A Crack in Histone Lysine Methylation , 2004, Cell.

[74]  J A Bailey,et al.  Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[75]  A. West,et al.  Calcium regulation of neuronal gene expression , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[76]  E. Vrba,et al.  Australopithecine enamel prism patterns. , 1978, Science.

[77]  S. Lowe,et al.  A microRNA polycistron as a potential human oncogene , 2005, Nature.

[78]  Keith D Robertson,et al.  Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery. , 2004, Nucleic acids research.

[79]  R. Tupler,et al.  Differential expression of the ICF (immunodeficiency, centromeric heterochromatin, facial anomalies) mutation in lymphocytes and fibroblasts. , 1989, Journal of medical genetics.

[80]  C. J. Barnes,et al.  Coregulators and chromatin remodeling in transcriptional control , 2004, Molecular carcinogenesis.

[81]  M. Ehrlich The ICF syndrome, a DNA methyltransferase 3B deficiency and immunodeficiency disease. , 2003, Clinical immunology.

[82]  Xiang-Jiao Yang,et al.  Class II Histone Deacetylases: from Sequence to Function, Regulation, and Clinical Implication , 2005, Molecular and Cellular Biology.

[83]  D. Bushnell,et al.  Structural basis of eukaryotic gene transcription , 2005, FEBS letters.

[84]  Jean Aicardi,et al.  A progressive syndrome of autism, dementia, ataxia, and loss of purposeful hand use in girls: Rett's syndrome: Report of 35 cases , 1983, Annals of neurology.

[85]  Eric P. Hoffman,et al.  Gene Expression Profiling in Postmortem Rett Syndrome Brain: Differential Gene Expression and Patient Classification , 2001, Neurobiology of Disease.