RNAs of the human chromosome 15q11-q13 imprinted region

Wiley Interdisciplinary Reviews: RNA

Volumn 4, Issue 2, 2013, Pages 155-166

  Chamberlain, Stormy J ^a  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

E6AP PROTEIN; LNCRNA; MICRORNA; NUCLEIC ACID; PIWI INTERACTING RNA; PROTEIN; RNA; SMALL NUCLEOLAR RNA; SNURF SNRPN PROTEIN; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

CHROMOSOME 15Q; GENE EXPRESSION; GENETIC CODE; GENOME IMPRINTING; HUMAN; HUMAN CHROMOSOME; HUMAN CHROMOSOME 15Q11 Q13; NONHUMAN; PRIORITY JOURNAL; REVIEW;

CHROMOSOMES, HUMAN, PAIR 15; GENOMIC IMPRINTING; HUMANS; RNA;

EID: 84874069570     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.1150     Document Type: Review

References (82)

1. Chamberlain SJ, Lalande M. Neurodevelopmental disorders involving genomic imprinting at human chromosome 15q11-q13. Neurobiol Dis 2010, 39:13-20.
2. Cattanach BM, Barr JA, Beechey CV, Martin J, Noebels J, Jones J. A candidate model for Angelman syndrome in the mouse. Mamm Genome 1997, 8:472-478.
3. Cattanach BM, Barr JA, Evans EP, Burtenshaw M, Beechey CV, Leff SE, Brannan CI, Copeland NG, Jenkins NA, Jones J. A candidate mouse model for Prader-Willi syndrome which shows an absence of Snrpn expression. Nat Genet 1992, 2:270-274.
4. Hogart A, Patzel KA, LaSalle JM. Gender influences monoallelic expression of ATP10A in human brain. Hum Genet 2008, 124:235-242.
5. Chai JH, Locke DP, Greally JM, Knoll JH, Ohta T, Dunai J, Yavor A, Eichler EE, Nicholls RD. Identification of four highly conserved genes between breakpoint hotspots BP1 and BP2 of the Prader-Willi/Angelman syndromes deletion region that have undergone evolutionary transposition mediated by flanking duplicons. Am J Hum Genet 2003, 73:898-925.
6. Ji Y, Eichler EE, Schwartz S, Nicholls RD. Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res 2000, 10:597-610.
7. Cassidy SB, Dykens E, Williams CA. Prader-Willi and Angelman syndromes: sister imprinted disorders. Am J Med Genet 2000, 97:136-146.
8. Amos-Landgraf JM, Ji Y, Gottlieb W, Depinet T, Wandstrat AE, Cassidy SB, Driscoll DJ, Rogan PK, Schwartz S, Nicholls RD. Chromosome breakage in the Prader-Willi and Angelman syndromes involves recombination between large, transcribed repeats at proximal and distal breakpoints. Am J Hum Genet 1999, 65:370-386.
9. Christian SL, Bhatt NK, Martin SA, Sutcliffe JS, Kubota T, Huang B, Mutirangura A, Chinault AC, Beaudet AL, Ledbetter DH. Integrated YAC contig map of the Prader-Willi/Angelman region on chromosome 15q11-q13 with average STS spacing of 35 kb. Genome Res 1998, 8:146-157.
10. Christian SL, Fantes JA, Mewborn SK, Huang B, Ledbetter DH. Large genomic duplicons map to sites of instability in the Prader-Willi/Angelman syndrome chromosome region (15q11-q13). Hum Mol Genet 1999, 8:1025-1037.
11. Reis A, Dittrich B, Greger V, Buiting K, Lalande M, Gillessen-Kaesbach G, Anvret M, Horsthemke B. Imprinting mutations suggested by abnormal DNA methylation patterns in familial Angelman and Prader-Willi syndromes. Am J Hum Genet 1994, 54:741-747.
12. Saitoh S, Buiting K, Rogan PK, Buxton JL, Driscoll DJ, Arnemann J, König R, Malcolm S, Horsthemke B, Nicholls RD. Minimal definition of the imprinting center and fixation of chromosome 15q11-q13 epigenotype by imprinting mutations. Proc Natl Acad Sci U S A 1996, 93:7811-7815.
13. Dubose AJ, Smith EY, Yang TP, Johnstone KA, Resnick JL. A new deletion refines the boundaries of the murine Prader-Willi syndrome imprinting center. Hum Mol Genet 2011, 20:3461-3466.
14. Rodriguez-Jato S, Nicholls RD, Driscoll DJ, Yang TP. Characterization of cis- and trans-acting elements in the imprinted human SNURF-SNRPN locus. Nucleic Acids Res 2005, 33:4740-4753.
15. Smith EY, Futtner CR, Chamberlain SJ, Johnstone KA, Resnick JL. Transcription is required to establish maternal imprinting at the Prader-Willi syndrome and Angelman syndrome locus. PLoS Genet 2011, 7:e1002422.
16. Xin Z, Allis CD, Wagstaff J. Parent-specific complementary patterns of histone H3 lysine 9 and H3 lysine 4 methylation at the Prader-Willi syndrome imprinting center. Am J Hum Genet 2001, 69:1389-1394.
17. Fulmer-Smentek SB, Francke U. Association of acetylated histones with paternally expressed genes in the Prader-Willi deletion region. Hum Mol Genet 2001, 10:645-652.
18. Chantalat S, Depaux A, Héry P, Barral S, Thuret JY, Dimitrov S, Gérard M. Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin. Genome Res 2011, 21:1426-1437.
19. Chai JH, Locke DP, Ohta T, Greally JM, Nicholls RD. Retrotransposed genes such as Frat3 in the mouse Chromosome 7C Prader- Willi syndrome region acquire the imprinted status of their insertion site. Mamm Genome 2001, 12:813-821.
20. Buiting K, Nazlican H, Galetzka D, Wawrzik M, Gross S, Horsthemke B. C15orf2 and a novel noncoding transcript from the Prader-Willi/Angelman syndrome region show monoallelic expression in fetal brain. Genomics 2007, 89:588-595.
21. Dubose AJ, Johnstone KA, Smith EY, Hallett RA, Resnick JL. Atp10a, a gene adjacent to the PWS/AS gene cluster, is not imprinted in mouse and is insensitive to the PWS-IC. Neurogenetics 2010, 11:145-51.
22. Kanber D. A paternal deletion of MKRN3, MAGEL2 and NDN does not result in Prader-Willi syndrome. Eur J Hum Genet 2009, 17:582-590.
23. Bohne A, Darras A, D'Cotta H, Baroiller JF, Galiana-Arnoux D, Volff JN. The vertebrate makorin ubiquitin ligase gene family has been shaped by large-scale duplication and retroposition from an ancestral gonad-specific, maternal-effect gene. BMC Genomics 2010, 11:721.
24. Boccaccio I, Glatt-Deeley H, Watrin F, Roëckel N, Lalande M, Muscatelli F. The human MAGEL2 gene and its mouse homologue are paternally expressed and mapped to the Prader-Willi region. Hum Mol Genet 1999, 8:2497-2505.
25. Bischof JM, Stewart CL, Wevrick R. Inactivation of the mouse Magel2 gene results in growth abnormalities similar to Prader-Willi syndrome. Hum Mol Genet 2007, 16:2713-2719.
26. Kozlov SV, Bogenpohl JW, Howell MP, Wevrick R, Panda S, Hogenesch JB, Muglia LJ, Van Gelder RN, Herzog ED, Stewart CL. The imprinted gene Magel2 regulates normal circadian output. Nat Genet 2007, 39:1266-1272.
27. Mercer RE, Wevrick R. Loss of magel2, a candidate gene for features of Prader-Willi syndrome, impairs reproductive function in mice. PLoS One 2009, 4:e4291.
28. Hayashi Y, Matsuyama K, Takagi K, Sugiura H, Yoshikawa K. Arrest of cell growth by necdin, a nuclear protein expressed in postmitotic neurons. Biochem Biophys Res Commun 1995, 213:317-324.
29. Taniura H, Taniguchi N, Hara M, Yoshikawa K. Necdin, a postmitotic neuron-specific growth suppressor, interacts with viral transforming proteins and cellular transcription factor E2F1. J Biol Chem 1998, 273:720-728.
30. Hasegawa K, Yoshikawa K. Necdin regulates p53 acetylation via Sirtuin1 to modulate DNA damage response in cortical neurons. J Neurosci 2008, 28:8772-8784.
31. Muscatelli F, Abrous DN, Massacrier A, Boccaccio I, Le Moal M, Cau P, Cremer H. Disruption of the mouse Necdin gene results in hypothalamic and behavioral alterations reminiscent of the human Prader-Willi syndrome. Hum Mol Genet 2000, 9:3101-3110.
32. Gerard M, Hernandez L, Wevrick R, Stewart CL. Disruption of the mouse necdin gene results in early post-natal lethality. Nat Genet 1999, 23:199-202.
33. Tsai TF, Armstrong D, Beaudet AL. Necdin-deficient mice do not show lethality or the obesity and infertility of Prader-Willi syndrome. Nat Genet 1999, 22:15-16.
34. Deponti D, François S, Baesso S, Sciorati C, Innocenzi A, Broccoli V, Muscatelli F, Meneveri R, Clementi E, Cossu G, Brunelli S. Necdin mediates skeletal muscle regeneration by promoting myoblast survival and differentiation. J Cell Biol 2007, 179:305-319.
35. Bush JR, Wevrick R. The Prader-Willi syndrome protein necdin interacts with the E1A-like inhibitor of differentiation EID-1 and promotes myoblast differentiation. Differentiation 2008, 76:994-1005.
36. Bush JR, Wevrick R. Loss of the Prader-Willi obesity syndrome protein necdin promotes adipogenesis. Gene 2012, 497:45-51.
37. Hasegawa K, Kawahara T, Fujiwara K, Shimpuku M, Sasaki T, Kitamura T, Yoshikawa K. Necdin controls Foxo1 acetylation in hypothalamic arcuate neurons to modulate the thyroid axis. J Neurosci 2012, 32:5562-5572.
38. Taniura H, Matsumoto K, Yoshikawa K. Physical and functional interactions of neuronal growth suppressor necdin with p53. J Biol Chem 1999, 274:16242-16248.
39. Lee S, Walker CL, Karten B, Kuny SL, Tennese AA, O'Neill MA, Wevrick R. Essential role for the Prader-Willi syndrome protein necdin in axonal outgrowth. Hum Mol Genet 2005, 14:627-637.
40. Wawrzik M, Unmehopa UA, Swaab DF, van de Nes J, Buiting K, Horsthemke B. The C15orf2 gene in the Prader-Willi syndrome region is subject to genomic imprinting and positive selection. Neurogenetics 2010, 11:153-161.
41. Royo H, Cavaille J. Non-coding RNAs in imprinted gene clusters. Biol Cell 2008, 100:149-166.
42. Neumann LC, Markaki Y, Mladenov E, Hoffmann D, Buiting K, Horsthemke B. The imprinted NPAP1/ C15orf2 gene in the Prader-Willi syndrome region encodes a nuclear pore complex associated protein. Hum Mol Genet 2012, 21:4038-48.
43. Gray TA, Saitoh S, Nicholls RD. An imprinted, mammalian bicistronic transcript encodes two independent proteins. Proc Natl Acad Sci U S A 1999, 96:5616-5621.
44. Huntriss JD, Latchman DS, Williams DG. The snRNP core protein SmB and tissue-specific SmN protein are differentially distributed between snRNP particles. Nucleic Acids Res 1993, 21:4047-4053.
45. Huibregtse JM, Scheffner M, Howley PM. Cloning and expression of the cDNA for E6-AP, a protein that mediates the interaction of the human papillomavirus E6 oncoprotein with p53. Mol Cell Biol 1993, 13:775-784.
46. Rougeulle C, Glatt H, Lalande M. The Angelman syndrome candidate gene, UBE3A/E6-AP, is imprinted in brain. Nat Genet 1997, 17:14-15.
47. Rougeulle C, Cardoso C, Fontes M, Colleaux L, Lalande M. An imprinted antisense RNA overlaps UBE3A and a second maternally expressed transcript. Nat Genet 1998, 19:15-16.
48. Chamberlain SJ, Brannan CI. The Prader-Willi syndrome imprinting center activates the paternally expressed murine Ube3a antisense transcript but represses paternal Ube3a. Genomics 2001, 73: 316-322.
49. Meng L, Person RE, Beaudet AL. Ube3a-ATS is an atypical RNA polymerase II transcript that represses the paternal expression of Ube3a. Hum Mol Genet 2012, 21:3001-12.
50. Kishino T, Lalande M, Wagstaff J. UBE3A/E6-AP mutations cause Angelman syndrome. Nat Genet 1997, 15:70-73.
51. Yamamoto Y, Huibregtse JM, Howley PM. The human E6-AP gene (UBE3A) encodes three potential protein isoforms generated by differential splicing. Genomics 1997, 41:263-266.
52. Jiang YH, Armstrong D, Albrecht U, Atkins CM, Noebels JL, Eichele G, Sweatt JD, Beaudet AL. Mutation of the Angelman ubiquitin ligase in mice causes increased cytoplasmic p53 and deficits of contextual learning and long-term potentiation. Neuron 1998, 21: 799-811.
53. Miura K, Kishino T, Li E, Webber H, Dikkes P, Holmes GL, Wagstaff J. Neurobehavioral and electroencephalographic abnormalities in Ube3a maternal-deficient mice. Neurobiol Dis 2002, 9:149-159.
54. Yashiro K, Riday TT, Condon KH, Roberts AC, Bernardo DR, Prakash R, Weinberg RJ, Ehlers MD, Philpot BD. Ube3a is required for experience-dependent maturation of the neocortex. Nat Neurosci 2009, 12:777-783.
55. Sato M, Stryker MP. Genomic imprinting of experience-dependent cortical plasticity by the ubiquitin ligase gene Ube3a. Proc Natl Acad Sci U S A 2010, 107:5611-5616.
56. Sutcliffe JS, Nakao M, Christian S, Orstavik KH, Tommerup N, Ledbetter DH, Beaudet AL. Deletions of a differentially methylated CpG island at the SNRPN gene define a putative imprinting control region. Nat Genet 1994, 8:52-58.
57. Yang T, Adamson TE, Resnick JL, Leff S, Wevrick R, Francke U, Jenkins NA, Copeland NG, Brannan CI. A mouse model for Prader-Willi syndrome imprinting-centre mutations. Nat Genet 1998, 19:25-31.
58. Bressler J, Tsai TF, Wu MY, Tsai SF, Ramirez MA, Armstrong D, Beaudet AL. The SNRPN promoter is not required for genomic imprinting of the Prader-Willi/Angelman domain in mice. Nat Genet 2001, 28:232-240.
59. Runte M, Hüttenhofer A, Gross S, Kiefmann M, Horsthemke B, Buiting K. The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum Mol Genet 2001, 10:2687-2700.
60. Ning Y, Roschke A, Christian SL, Lesser J, Sutcliffe JS, Ledbetter DH. Identification of a novel paternally expressed transcript adjacent to snRPN in the Prader-Willi syndrome critical region. Genome Res 1996, 6:742-746.
61. Jong MT, Carey AH, Caldwell KA, Lau MH, Handel MA, Driscoll DJ, Stewart CL, Rinchik EM, Nicholls RD. Imprinting of a RING zinc-finger encoding gene in the mouse chromosome region homologous to the Prader-Willi syndrome genetic region. Hum Mol Genet 1999, 8:795-803.
62. Castle JC, Armour CD, Löwer M, Haynor D, Biery M, Bouzek H, Chen R, Jackson S, Johnson JM, Rohl CA, Raymond CK. Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification. PLoS One 2010, 5:e11779.
63. Buiting K, Barnicoat A, Lich C, Pembrey M, Malcolm S, Horsthemke B. Disruption of the bipartite imprinting center in a family with Angelman syndrome. Am J Hum Genet 2001, 68:1290-1294.
64. Wevrick R, Kerns JA, Francke U. Identification of a novel paternally expressed gene in the Prader-Willi-Syndrome region. Hum Mol Genet 1994, 3:1877-1882.
65. Landers M, Bancescu DL, Le Meur E, Rougeulle C, Glatt-Deeley H, Brannan C, Muscatelli F, Lalande M. Regulation of the large (approximately 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn. Nucleic Acids Res 2004, 32:3480-3492.
66. Cavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI, Horsthemke B, Bachellerie JP, Brosius J, Hüttenhofer A. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc Natl Acad Sci U S A 2000, 97:14311-14316.
67. Chamberlain SJ, Chen PF, Ng KY, Bourgois-Rocha F, Lemtiri-Chlieh F, Levine ES, Lalande M. Induced pluripotent stem cell models of the genomic imprinting disorders Angelman and Prader-Willi syndromes. Proc Natl Acad Sci U S A 2010, 107:17668-17673.
68. Wevrick R, Francke U. An imprinted mouse transcript homologous to the human imprinted in Prader-Willi syndrome (IPW) gene. Hum Mol Genet 1997, 6:325-332.
69. Farber C, Dittrich B, Buiting K, Horsthemke B. The chromosome 15 imprinting centre (IC) region has undergone multiple duplication events and contains an upstream exon of SNRPN that is deleted in all Angelman syndrome patients with an IC microdeletion. Hum Mol Genet 1999, 8:337-343.
70. Numata K, Kohama C, Abe K, Kiyosawa H. Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription. Nucleic Acids Res 2011, 39:2649-2657.
71. Kishore S, Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 2006, 311:230-232.
72. Vitali P, Basyuk E, Le Meur E, Bertrand E, Muscatelli F, Cavaillé J, Huttenhofer A. ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs. J Cell Biol 2005, 169:745-753.
73. Bortolin-Cavaille ML, Cavaille J. The SNORD115 (H/MBII-52) and SNORD116 (H/MBII-85) gene clusters at the imprinted Prader-Willi locus generate canonical box C/D snoRNAs. Nucleic Acids Res 2012, 40:6800-7.
74. Yin QF, Yang L, Zhang Y, Xiang J-F, Wu Y-W, Carmichael GG, Chen L-L. Long noncoding RNAs with snoRNA ends. Mol Cell 2012, 48:219-30.
75. Girard A, Sachidanandam R, Hannon GJ, Carmell MA. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 2006, 442:199-202.
76. Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, Choi WW, Au WY, Srivastava G, Czader MB, Rizzieri DA, et al. Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. Blood 2010, 116:e118-e127.
77. Jong MT, Gray TA, Ji Y, Glenn CC, Saitoh S, Driscoll DJ, Nicholls RD. A novel imprinted gene, encoding a RING zinc-finger protein, and overlapping antisense transcript in the Prader-Willi syndrome critical region. Hum Mol Genet 1999, 8:783-793.
78. Jay P, Rougeulle C, Massacrier A, Moncla A, Mattei MG, Malzac P, Roëckel N, Taviaux S, Lefranc JL, Cau P, et al. The human necdin gene, NDN, is maternally imprinted and located in the Prader-Willi syndrome chromosomal region. Nat Genet 1997, 17:357-361.
79. van Amerongen R, van der Gulden H, Bleeker F, Jonkers J, Berns A. Characterization and functional analysis of the murine Frat2 gene. J Biol Chem 2004, 279:26967-26974.
80. Glatt-Deeley H, Bancescu DL, Lalande M. Prader-Willi syndrome, Snord115, and Htr2c editing. Neurogenetics 2009, 11:143-4.
81. Kishore S, Khanna A, Zhang Z, Hui J, Balwierz PJ, Stefan M, Beach C, Nicholls RD, Zavolan M, Stamm S. The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum Mol Genet 2010, 19:1153-1164.
82. Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, et al. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 2010, 24:992-1009.