The Mendelian disorders of the epigenetic machinery

Genome Research

Volumn 25, Issue 10, 2015, Pages 1473-1481

  Bjornsson, Hans Tomas ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE DEACETYLASE;

ALLELE; CELL POPULATION; CELLS BY BODY ANATOMY; CLINICAL FEATURE; ENZYME INHIBITION; EPIGENETICS; GENE DOSAGE; GENE EXPRESSION; GENE LOSS; GENE SEQUENCE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC DISORDER; HUMAN; INTELLECTUAL IMPAIRMENT; KABUKI MAKEUP SYNDROME; MENDELIAN DISORDER; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; REVIEW; RUBINSTEIN SYNDROME; ANIMAL; GENETIC EPIGENESIS; GENETIC PREDISPOSITION; GENETICS; MUTATION; NEUROLOGIC DISEASE;

ANIMALS; EPIGENESIS, GENETIC; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MUTATION; NERVOUS SYSTEM DISEASES;

EID: 84942924098     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.190629.115     Document Type: Review

References (68)

1. Alarcón JM, Malleret G, Touzani K, Vronskaya S, Ishii S, Kandel ER, Barco A. 2004. Chromatin acetylation, memory, and LTP are impaired in CBP+/- mice: a model for the cognitive deficit in Rubinstein-Taybi syndrome and its amelioration. Neuron 42: 947-959.
2. Almuriekhi M, Shintani T, Fahiminiya S, Fujikawa A, Kuboyama K, Takeuchi Y, Nawaz Z, Nadaf J, Kamel H, Kitam AK, et al. 2015. Loss-of-function mutation in APC2 causes Sotos syndrome features. Cell Rep 10: 1585-1589.
3. Baets J, Duan X, Wu Y, Smith G, Seeley WW, Mademan I, McGrath NM, Beadell NC, Khoury J, Botuyan MV, et al. 2015. Defects of mutant DNMT1 are linked to a spectrum of neurological disorders. Brain 138: 845-861.
4. Baker LA, Allis CD, Wang GG. 2008. PHD fingers in human diseases: disorders arising from misinterpreting epigenetic marks. Mutat Res 647: 3-12.
5. Balemans MC, Ansar M, Oudakker AR, van Caam AP, Bakker B, Vitters EL, van der Kraan PM, de Bruijn DR, Janssen SM, Kuipers AJ, et al. 2014. Reduced euchromatin histone methyltransferase 1 causes developmental delay, hypotonia, and cranial abnormalities associated with increased bone gene expression in Kleefstra syndrome mice. Dev Biol 386: 395-407.
6. Banka S, Howard E, Bunstone S, Chandler KE, Kerr B, Lachlan K, McKee S, Mehta SG, Tavares AL, Tolmie J, et al. 2013. MLL2 mosaic mutations and intragenic deletion-duplications in patients with Kabuki syndrome. Clin Genet 83: 467-471.
7. Baujat G, Cormier-Daire V. 2007. Sotos syndrome. Orphanet J Rare Dis 2: 36.
8. Berdasco M, Esteller M. 2013. Genetic syndromes caused by mutations in epigenetic genes. Hum Genet 132: 359-383.
9. Bjornsson HT, Benjamin JS, Zhang L, Weissman J, Gerber EE, Chen YC, Vaurio RG, Potter MC, Hansen KD, Dietz HC. 2014. Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome. Sci Transl Med 6: 256ra135.
10. Borel C, Ferreira PG, Santoni F, Delaneau O, Fort A, Popadin KY, Garieri M, Falconnet E, Ribaux P, Guipponi M, et al. 2015. Biased allelic expression in human primary fibroblast single cells. Am J Hum Genet 96: 70-80.
11. Cai L, Dalal CK, Elowitz MB. 2008. Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 455: 485-490.
12. Clapier CR, Cairns BR. 2009. The biology of chromatin remodeling complexes. Annu Rev Biochem 78: 273-304.
13. Clynes D, Jelinska C, Xella B, Ayyub H, Taylor S, Mitson M, Bachrati CZ, Higgs DR, Gibbons RJ. 2014. ATRX dysfunction induces replication defects in primary mouse cells. PLoS One 9: e92915.
14. Crabtree GR, Graef IA. 2008. Bursting into the nucleus. Sci Signal 1: pe54.
15. De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, et al. 2014. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 515: 209-215.
16. DeardorffMA, Bando M, Nakato R, Watrin E, Itoh T, Minamino M, Saitoh K, Komata M, Katou Y, Clark D, et al. 2012. HDAC8 mutations in Cornelia de Lange syndrome affect the cohesion acetylation cycle. Nature 489: 313-317.
17. Dentici ML, Di Pede A, Lepri FR, Gnazzo M, Lombardi MH, Auriti C, Petrocchi S, Pisaneschi E, Bellacchio E, Capolino R, et al. 2015. Kabuki syndrome: clinical and molecular diagnosis in the first year of life. Arch Dis Child 100: 158-164.
18. Eissenberg JC. 2012. Structural biology of the chromodomain: form and function. Gene 496: 69-78.
19. Fahrner JA, Bjornsson HT. 2014. Mendelian disorders of the epigenetic machinery: tipping the balance of chromatin states. Annu Rev Genomics Hum Genet 15: 269-293.
20. Ficz G, Heintzmann R, Arndt-Jovin DJ. 2005. Polycomb group protein complexes exchange rapidly in living Drosophila. Development 132: 3963-3976.
21. Gibson WT, Hood RL, Zhan SH, Bulman DE, Fejes AP, Moore R, Mungall AJ, Eydoux P, Babul-Hirji R, An J, et al. 2012. Mutations in EZH2 cause Weaver syndrome. Am J Hum Genet 90: 110-118.
22. Greenleaf WJ. 2015. Assaying the epigenome in limited numbers of cells. Methods 72: 51-56.
23. Guy J, Gan J, Selfridge J, Cobb S, Bird A. 2007. Reversal of neurological defects in a mouse model of Rett syndrome. Science 315: 1143-1147.
24. Hanson RD, Hess JL, Yu BD, Ernst P, van Lohuizen M, Berns A, van der Lugt NM, Shashikant CS, Ruddle FH, Seto M, et al. 1999. Mammalian Trithorax and Polycomb-group homologues are antagonistic regulators of homeotic development. Proc Natl Acad Sci 96: 14372-14377.
25. Harrison SJ, Nishinakamura R, Jones KR, Monaghan AP. 2012. Sall1 regulates cortical neurogenesis and laminar fate specification in mice: implications for neural abnormalities in Townes-Brocks syndrome. Dis Model Mech 5: 351-365.
26. Horsfield JA, Print CG, MönnichM. 2012. Diverse developmental disorders from the one ring: Distinct molecular pathways underlie the cohesinopathies. Front Genet 3: 171.
27. Jimenez-Sanchez G, Childs B, Valle D. 2001. Human disease genes. Nature 409: 853-855.
28. Jin B, Tao Q, Peng J, Soo HM,WuW, Ying J, Fields CR, Delmas AL, Liu X, Qiu J, et al. 2008. DNA methyltransferase 3B (DNMT3B) mutations in ICF syndrome lead to altered epigenetic modifications and aberrant expression of genes regulating development, neurogenesis and immune function. Hum Mol Genet 17: 690-709.
29. Jones WD, Dafou D, McEntagart M, Woollard WJ, Elmslie FV, Holder- Espinasse M, Irving M, Saggar AK, Smithson S, Trembath RC, et al. 2012. De novo mutations in MLL cause Wiedemann-Steiner syndrome. Am J Hum Genet 91: 358-364.
30. Jørgensen HF, Bird A. 2002. MeCP2 and other methyl-CpG binding proteins. Ment Retard Dev Disabil Res Rev 8: 87-93.
31. Jurkowska RZ, Jurkowski TP, Jeltsch A. 2011. Structure and function of mammalian DNA methyltransferases. Chembiochem 12: 206-222.
32. Kleefstra T, Brunner HG, Amiel J, Oudakker AR, Nillesen WM, Magee A, Geneviève D, Cormier-Daire V, van Esch H, Fryns JP, et al. 2006. Lossof- function mutations in euchromatin histone methyltransferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. Am J Hum Genet 79: 370-377.
33. Kleefstra T, Schenck A, Kramer JM, van Bokhoven H. 2014. The genetics of cognitive epigenetics. Neuropharmacology 80: 83-94.
34. Korzus E, Rosenfeld MG, Mayford M. 2004. CBP histone acetyltransferase activity is a critical component of memory consolidation. Neuron 42: 961-972.
35. Lalani SR, Safiullah AM, Molinari LM, Fernbach SD, Martin DM, Belmont JW. 2004. SEMA3E mutation in a patient with CHARGE syndrome. J Med Genet 41: e94.
36. Law MJ, Lower KM, Voon HP, Hughes JR, Garrick D, Viprakasit V, Mitson M, De Gobbi M, Marra M, Morris A, et al. 2010. ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner. Cell 143: 367-378.
37. Leduc MS, Beuten J, Zhang J, Niu Z, Xia F, Landsverk M, Bekheirnia MR, AlcarazW, Cui H, Walkiewicz MA, et al. 2014. Clinical whole exome sequencing provides insight on the prevalence of chromatin remodeling genes in the context of intellectual disability. In 2014 ACMG Annual Clinical Genetics Meeting: Abstract 290. American College of Medical Genetics and Genomics, Bethesda, MD.
38. Levenson JM, Roth TL, Lubin FD, Miller CA, Huang IC, Desai P, Malone LM, Sweatt JD. 2006. Evidence that DNA (cytosine-5) methyltransferase regulates synaptic plasticity in the hippocampus. J Biol Chem 281: 15763-15773.
39. Lopez-Atalaya JP, Ciccarelli A, Viosca J, Valor LM, Jimenez-Minchan M, Canals S, Giustetto M, Barco A. 2011. CBP is required for environmental enrichment-induced neurogenesis and cognitive enhancement. EMBO J 30: 4287-4298.
40. Mielcarek M, Seredenina T, Stokes MP, Osborne GF, Landles C, Inuabasi L, Franklin SA, Silva JC, Luthi-Carter R, Beaumont V, et al. 2013. HDAC4 does not act as a protein deacetylase in the postnatal murine brain in vivo. PLoS One 8: e80849.
41. Miska EA, Karlsson C, Langley E, Nielsen SJ, Pines J, Kouzarides T. 1999. HDAC4 deacetylase associates with and represses the MEF2 transcription factor. EMBO J 18: 5099-5107.
42. Mito Y, Henikoff JG, Henikoff S. 2007. Histone replacement marks the boundaries of cis-regulatory domains. Science 315: 1408-1411.
43. Montaño CM, Irizarry RA, Kaufmann WE, Talbot K, Gur RE, Feinberg AP, Taub MA. 2013. Measuring cell-type specific differential methylation in human brain tissue. Genome Biol 14: R94.
44. Morice E, Farley S, Poirier R, Dallerac G, Chagneau C, Pannetier S, Hanauer A, Davis S, Vaillend C, Laroche S. 2013. Defective synaptic transmission and structure in the dentate gyrus and selective fear memory impairment in the Rsk2 mutant mouse model of Coffin-Lowry syndrome. Neurobiol Dis 58: 156-168.
45. Moriya J, Minamino T, Tateno K, Okada S, Uemura A, Shimizu I, Yokoyama M, Nojima A, Okada M, Koga H, et al. 2010. Inhibition of semaphorin as a novel strategy for therapeutic angiogenesis. Circ Res 106: 391-398.
46. Mullegama SV, Pugliesi L, Burns B, Shah Z, Tahir R, Gu Y, Nelson DL, Elsea SH. 2015. MBD5 haploinsufficiency is associated with sleep disturbance and disrupts circadian pathways common to Smith-Magenis and fragile X syndromes. Eur J Hum Genet 23: 781-789.
47. Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, et al. 2010. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42: 790-793.
48. Paro R. 1995. Propagatingmemory of transcriptional states. Trends Genet 11: 295-297.
49. Ptashne M. 2013. Epigenetics: core misconcept. Proc Natl Acad Sci 110: 7101-7103.
50. Ritchie K, Watson LA, Davidson B, Jiang Y, Bérubé NG. 2014. ATRX is required for maintenance of the neuroprogenitor cell pool in the embryonic mouse brain. Biol Open 3: 1158-1163.
51. Ronan JL, Wu W, Crabtree GR. 2013. From neural development to cognition: unexpected roles for chromatin. Nat Rev Genet 14: 347-359.
52. Russo VEA, Martienssen RA, Riggs AD. 1996. Epigenetic mechanisms of gene regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
53. Sanchez R, Zhou MM. 2009. The role of human bromodomains in chromatin biology and gene transcription. Curr Opin Drug Discov Devel 12: 659-665.
54. Sando R III, Gounko N, Pieraut S, Liao L, Yates J III, Maximov A. 2012. HDAC4 governs a transcriptional program essential for synaptic plasticity and memory. Cell 151: 821-834.
55. Schulz Y, Freese L, Mänz J, Zoll B, Völter C, Brockmann K, Bögershausen N, Becker J, Wollnik B, Pauli S. 2014. CHARGE and Kabuki syndromes: a phenotypic and molecular link. Hum Mol Genet 23: 4396-4405.
56. Schwartz YB, Pirrotta V. 2008. Polycomb complexes and epigenetic states. Curr Opin Cell Biol 20: 266-273.
57. Shi D, Pop MS, Kulikov R, Love IM, Kung AL, Grossman SR. 2009. CBP and p300 are cytoplasmic E4 polyubiquitin ligases for p53. Proc Natl Acad Sci 106: 16275-16280.
58. Singer ZS, Yong J, Tischler J, Hackett JA, Altinok A, Surani MA, Cai L, Elowitz MB. 2014. Dynamic heterogeneity and DNA methylation in embryonic stem cells. Mol Cell 55: 319-331.
59. Tahiliani M, Koh KP, Shen Y, PastorWA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. 2009. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324: 930-935.
60. Tatton-Brown K, Seal S, Ruark E, Harmer J, Ramsay E, Del Vecchio Duarte S, Zachariou A, Hanks S, O'Brien E, Aksglaede L, et al. 2014. Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability. Nat Genet 46: 385-388.
61. Tsai HC, Baylin SB. 2011. Cancer epigenetics: linking basic biology to clinical medicine. Cell Res 21: 502-517.
62. Valor LM, Pulopulos MM, Jimenez-Minchan M, Olivares R, Lutz B, Barco A. 2011. Ablation of CBP in forebrain principal neurons causes modest memory and transcriptional defects and a dramatic reduction of histone acetylation but does not affect cell viability. J Neurosci 31: 1652-1663.
63. Van Nostrand JL, Brady CA, Jung H, Fuentes DR, Kozak MM, Johnson TM, Lin CY, Lin CJ, Swiderski DL, Vogel H, et al. 2014. Inappropriate p53 activation during development induces features of CHARGE syndrome. Nature 514: 228-232.
64. Vega RB, Matsuda K, Oh J, Barbosa AC, Yang X, Meadows E, McAnally J, Pomajzl C, Shelton JM, Richardson JA, et al. 2004. Histone deacetylase 4 controls chondrocyte hypertrophy during skeletogenesis. Cell 119: 555-566.
65. Williams SR, Aldred MA, Der Kaloustian VM, Halal F, Gowans G, McLeod DR, Zondag S, Toriello HV, Magenis RE, Elsea SH. 2010. Haploinsufficiency of HDAC4 causes brachydactyly mental retardation syndrome, with brachydactyly type E, developmental delays, and behavioral problems. Am J Hum Genet 87: 219-228.
66. Xing J, Ginty DD, Greenberg ME. 1996. Coupling of the RAS-MAPK pathway to gene activation by RSK2, a growth factor-regulated CREB kinase. Science 273: 959-963.
67. Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, et al. 2013. De novo mutations in histone-modifying genes in congenital heart disease. Nature 498: 220-223.
68. Zhang J, Ji F, Liu Y, Lei X, Li H, Ji G, Yuan Z, Jiao J. 2014. Ezh2 regulates adult hippocampal neurogenesis and memory. J Neurosci 34: 5184-5199.