Allele-Biased Expression in Differentiating Human Neurons: Implications for Neuropsychiatric Disorders

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Lin, Mingyan ^a   Hrabovsky, Anastasia ^a   Pedrosa, Erika ^a   Wang, Tao ^a   Zheng, Deyou ^a   Lachman, Herbert M ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 4; NEUROLIGIN 1;

A2BP1 GENE; ALLELE; ANIMAL CELL; ARTICLE; AUTISM; CONTROLLED STUDY; DISEASE TRANSMISSION; EMBRYO; ERBB4 GENE; FEMALE; GENE; GENE EXPRESSION; GENE SEQUENCE; GENOME IMPRINTING; HUMAN; HUMAN CELL; MALE; MENTAL DISEASE; MONOZYGOTIC TWINS; MOUSE; NERVE CELL DIFFERENTIATION; NLGN1 GENE; NLGN4X GENE; NONHUMAN; NRG1 GENE; NRG3 GENE; NRXN1 GENE; NUCLEOTIDE SEQUENCE; PENETRANCE; PLURIPOTENT STEM CELL; SCHIZOPHRENIA; TRANSCRIPTOMICS; TWIN DISCORDANCE;

ALLELES; BASE SEQUENCE; CHILD; CHILD DEVELOPMENT DISORDERS, PERVASIVE; HUMANS; INDUCED PLURIPOTENT STEM CELLS; MENTAL DISORDERS; NEUROGENESIS; NEURONS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SCHIZOPHRENIA; TRANSCRIPTOME;

EID: 84865839318     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044017     Document Type: Article

References (58)

1. Delaval K, Feil R, (2004) Epigenetic regulation of mammalian genomic imprinting. Curr Opin Genet Dev 14(2) 188-195: 10.1016/j.gde.2004.01.005.
2. Holmes R, Soloway PD, (2006) Regulation of imprinted DNA methylation. Cytogenet Genome Res 113(1-4) 122-129: 10.1159/000090823.
3. Ideraabdullah FY, Vigneau S, Bartolomei MS, (2008) Genomic imprinting mechanisms in mammals. Mutat Res 647(1-2) 77-85: 10.1016/j.mrfmmm.2008.08.008.
4. Radford EJ, Ferron SR, Ferguson-Smith AC, (2011) Genomic imprinting as an adaptative model of developmental plasticity. FEBS Lett 585(13) 2059-2066: 10.1016/j.febslet.2011.05.063.
5. Edwards CA, Rens W, Clarke O, Mungall AJ, Hore T, et al. (2007) The evolution of imprinting: Chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals. BMC Evol Biol 7 157: 10.1186/1471-2148-7-157.
6. Gregg C, Zhang J, Butler JE, Haig D, Dulac C, (2010) Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329(5992) 682-685: 10.1126/science.1190831.
7. Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, et al. (2010) High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329(5992) 643-648: 10.1126/science.1190830.
8. Deveale B, van der Kooy D, Babak T, (2012) Critical evaluation of imprinted gene expression by RNA-seq: A new perspective. PLoS Genet 8(3) e1002600: 10.1371/journal.pgen.1002600.
9. Cassidy SB, Schwartz S, Miller JL, Driscoll DJ (2011) Prader-willi syndrome. Genet Med. 10.1097/GIM.0b013e31822bead0.
10. Fradin D, Cheslack-Postava K, Ladd-Acosta C, Newschaffer C, Chakravarti A, et al. (2010) Parent-of-origin effects in autism identified through genome-wide linkage analysis of 16,000 SNPs. PLoS One 5(9) e12513: 10.1371/journal.pone.0012513.
11. Francks C, Tozzi F, Farmer A, Vincent JB, Rujescu D, et al. (2008) Population-based linkage analysis of schizophrenia and bipolar case-control cohorts identifies a potential susceptibility locus on 19q13. Mol Psychiatry. 10.1038/mp.2008.100.
12. Berrettini WH, Ferraro TN, Goldin LR, Weeks DE, Detera-Wadleigh S, et al. (1994) Chromosome 18 DNA markers and manic-depressive illness: Evidence for a susceptibility gene. Proc Natl Acad Sci U S A 91(13): 5918-5921.
13. Ingason A, Kirov G, Giegling I, Hansen T, Isles AR, et al. (2011) Maternally derived microduplications at 15q11-q13: Implication of imprinted genes in psychotic illness. Am J Psychiatry 168(4) 408-417: 10.1176/appi.ajp.2010.09111660.
14. Crespi B, Badcock C, (2008) Psychosis and autism as diametrical disorders of the social brain. Behav Brain Sci 31(3): 241-61; discussion 261-320: 10.1017/S0140525X08004214.
15. Badcock C, Crespi B, (2006) Imbalanced genomic imprinting in brain development: An evolutionary basis for the aetiology of autism. J Evol Biol 19(4): 1007-1032. 10 (1111/j.1420-9101.2006.01091) ():: x.
16. Kopsida E, Mikaelsson MA, Davies W, (2011) The role of imprinted genes in mediating susceptibility to neuropsychiatric disorders. Horm Behav 59(3) 375-382: 10.1016/j.yhbeh.2010.04.005.
17. Pun FW, Zhao C, Lo WS, Ng SK, Tsang SY, et al. (2011) Imprinting in the schizophrenia candidate gene GABRB2 encoding GABA(A) receptor beta(2) subunit. Mol Psychiatry 16(5) 557-568: 10.1038/mp.2010.47.
18. Kitsiou-Tzeli S, Tzetis M, Sofocleous C, Vrettou C, Xaidara A, et al. (2010) De novo interstitial duplication of the 15q11.2-q14 PWS/AS region of maternal origin: Clinical description, array CGH analysis, and review of the literature. Am J Med Genet A 152A(8) 1925-1932: 10.1002/ajmg.a.33447.
19. Kwasnicka-Crawford DA, Roberts W, Scherer SW, (2007) Characterization of an autism-associated segmental maternal heterodisomy of the chromosome 15q11-13 region. J Autism Dev Disord 37(4) 694-702: 10.1007/s10803-006-0225-8.
20. Simic M, Turk J, (2004) Autistic spectrum disorder associated with partial duplication of chromosome 15; three case reports. Eur Child Adolesc Psychiatry 13(6) 389-393: 10.1007/s00787-004-0414-y.
21. Wilkins JF, (2010) Antagonistic coevolution of two imprinted loci with pleiotropic effects. Evolution 64(1): 142-151. 10 (1111/j.1558-5646.2009.00826) ():: x.
22. Smit H, (2010) A conceptual contribution to battles in the brain. Biol Philos 25(5) 803-821: 10.1007/s10539-010-9195-5.
23. Roppolo D, Vollery S, Kan CD, Luscher C, Broillet MC, et al. (2007) Gene cluster lock after pheromone receptor gene choice. EMBO J 26(14) 3423-3430: 10.1038/sj.emboj.7601782.
24. Krueger C, Morison IM, (2008) Random monoallelic expression: Making a choice. Trends Genet 24(6) 257-259: 10.1016/j.tig.2008.03.005.
25. Magklara A, Yen A, Colquitt BM, Clowney EJ, Allen W, et al. (2011) An epigenetic signature for monoallelic olfactory receptor expression. Cell 145(4) 555-570: 10.1016/j.cell.2011.03.040.
26. Yagi T, (2008) Clustered protocadherin family. Dev Growth Differ 50 Suppl 1: S131-40. 10 (1111/j.1440-169X.2008.00991) ():: x.
27. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A, (2007) Widespread monoallelic expression on human autosomes. Science 318(5853) 1136-1140: 10.1126/science.1148910.
28. Gottesman II, Bertelsen A, (1989) Confirming unexpressed genotypes for schizophrenia. risks in the offspring of Fischer's Danish identical and fraternal discordant twins. Arch Gen Psychiatry 46(10): 867-872.
29. Folstein S, Rutter M, (1977) Infantile autism: A genetic study of 21 twin pairs. J Child Psychol Psychiatry 18(4): 297-321.
30. Allen MG, (1976) Twin studies of affective illness. Arch Gen Psychiatry 33(12): 1476-1478.
31. Tsuang M, (2000) Schizophrenia: Genes and environment. Biol Psychiatry 47(3): 210-220.
32. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, et al. (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131(5) 861-872: 10.1016/j.cell.2007.11.019.
33. Brennand KJ, Simone A, Jou J, Gelboin-Burkhart C, Tran N, et al. (2011) Modelling schizophrenia using human induced pluripotent stem cells. Nature. 10.1038/nature09915.
34. Marchetto MC, Carromeu C, Acab A, Yu D, Yeo GW, et al. (2010) A model for neural development and treatment of rett syndrome using human induced pluripotent stem cells. Cell 143(4) 527-539: 10.1016/j.cell.2010.10.016.
35. Chiang CH, Su Y, Wen Z, Yoritomo N, Ross CA, et al. (2011) Integration-free induced pluripotent stem cells derived from schizophrenia patients with a DISC1 mutation. Mol Psychiatry. 10.1038/mp.2011.13.
36. Lin M, Pedrosa E, Shah A, Hrabovsky A, Maqbool S, et al. (2011) RNA-seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. PLoS One 6(9) e23356: 10.1371/journal.pone.0023356.
37. Pedrosa E, Sandler V, Shah A, Carroll R, Chang C, et al. (2011) Development of patient-specific neurons in schizophrenia using induced pluripotent stem cells. J Neurogenet. 10.3109/01677063.2011.597908.
38. Ginsberg SD, Mirnics K, (2006) Functional genomic methodologies. Prog Brain Res 158 15-40: 10.1016/S0079-6123(06)58002-1.
39. Deep-Soboslay A, Iglesias B, Hyde TM, Bigelow LB, Imamovic V, et al. (2008) Evaluation of tissue collection for postmortem studies of bipolar disorder. Bipolar Disord 10(7): 822-828. 10 (1111/j.1399-5618.2008.00607) ():: x.
40. Hill C, Keks N, Roberts S, Opeskin K, Dean B, et al. (1996) Problem of diagnosis in postmortem brain studies of schizophrenia. Am J Psychiatry 153(4): 533-537.
41. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321(5891) 956-960: 10.1126/science.1160342.
42. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y, (2008) RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18(9) 1509-1517: 10.1101/gr.079558.108.
43. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5(7) 621-628: 10.1038/nmeth.1226.
44. Feng J, Li W, Jiang T, (2011) Inference of isoforms from short sequence reads. J Comput Biol 18(3) 305-321: 10.1089/cmb.2010.0243.
45. Li SM, Valo Z, Wang J, Gao H, Bowers CW, et al. (2012) Transcriptome-wide survey of mouse CNS-derived cells reveals monoallelic expression within novel gene families. PLoS One 7(2) e31751: 10.1371/journal.pone.0031751.
46. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3) R25: 10.1186/gb-2009-10-3-r25.
47. Heap GA, Yang JH, Downes K, Healy BC, Hunt KA, et al. (2010) Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum Mol Genet 19(1) 122-134: 10.1093/hmg/ddp473.
48. Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, et al. (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 25(24) 3207-3212: 10.1093/bioinformatics/btp579.
49. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The sequence Alignment/Map format and SAMtools. Bioinformatics 25(16) 2078-2079: 10.1093/bioinformatics/btp352.
50. Benjamini Y, Heller R, Yekutieli D, (2009) Selective inference in complex research. Philos Transact A Math Phys Eng Sci 367(1906) 4255-4271: 10.1098/rsta.2009.0127.
51. Hochberg Y, Benjamini Y, (1990) More powerful procedures for multiple significance testing. Stat Med 9(7): 811-818.
52. Tchieu J, Kuoy E, Chin MH, Trinh H, Patterson M, et al. (2010) Female human iPSCs retain an inactive X chromosome. Cell Stem Cell 7(3) 329-342: 10.1016/j.stem.2010.06.024.
53. Bruck T, Benvenisty N, (2011) Meta-analysis of the heterogeneity of X chromosome inactivation in human pluripotent stem cells. Stem Cell Res 6(2) 187-193: 10.1016/j.scr.2010.12.001.
54. Kim DH, Jeon Y, Anguera MC, Lee JT (2011) X-chromosome epigenetic reprogramming in pluripotent stem cells via noncoding genes. Semin Cell Dev Biol. 10.1016/j.semcdb.2011.02.025.
55. Kim KP, Thurston A, Mummery C, Ward-van Oostwaard D, Priddle H, et al. (2007) Gene-specific vulnerability to imprinting variability in human embryonic stem cell lines. Genome Res 17(12) 1731-1742: 10.1101/gr.6609207.
56. Oudejans CB, Mulders J, Lachmeijer AM, van Dijk M, Konst AA, et al. (2004) The parent-of-origin effect of 10q22 in pre-eclamptic females coincides with two regions clustered for genes with down-regulated expression in androgenetic placentas. Mol Hum Reprod 10(8) 589-598: 10.1093/molehr/gah080.
57. Miyanari Y, Torres-Padilla ME (2012) Control of ground-state pluripotency by allelic regulation of nanog. Nature. 10.1038/nature10807; 10.1038/nature10807.
58. Huang HS, Allen JA, Mabb AM, King IF, Miriyala J, et al. (2011) Topoisomerase inhibitors unsilence the dormant allele of Ube3a in neurons. Nature 21;481(7380): 185-189. Source 10.1038/nature10726.