Autosomal monoallelic expression: Genetics of epigenetic diversity?

Current Opinion in Genetics and Development

Volumn 23, Issue 6, 2013, Pages 642-648

  Savova, Virginia ^a   Vigneau, Sébastien ^b,c   Gimelbrant, Alexander A ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOSOMAL MONOALLELIC EXPRESSION; BINDING SITE; CELL POPULATION; DEVELOPMENTAL STAGE; EPIGENETICS; GENE EXPRESSION; GENE LOCUS; GENETIC HETEROGENEITY; GENETIC REGULATION; GENETIC STABILITY; GENETIC VARIABILITY; GENOME IMPRINTING; GENOTYPE PHENOTYPE CORRELATION; HAPLOINSUFFICIENCY; HUMAN; MITOSIS; MOLECULAR CLONING; MOSAICISM; NONHUMAN; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; STABLE EXPRESSION; TRANSCRIPTION REGULATION; X CHROMOSOME INACTIVATION;

ALLELES; ANIMALS; EPIGENESIS, GENETIC; GENE EXPRESSION; GENETIC VARIATION; GENOME; HAPLOINSUFFICIENCY; HUMANS; MODELS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 84889589801     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2013.09.001     Document Type: Review

References (58)

1. Lyon M.F. Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature 1961, 190:372-373.
2. Carrel L., Willard H.F. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 2005, 434:400-404.
3. Berletch J.B., Yang F., Disteche C.M. Escape from X inactivation in mice and humans. Genome Biol 2010, 11:213.
4. Yang F., Babak T., Shendure J., Disteche C.M. Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Res 2010, 20:614-622.
5. Abramowitz L.K., Bartolomei M.S. Genomic imprinting: recognition and marking of imprinted loci. Curr Opin Genet Dev 2012, 22:72-78.
6. Gimelbrant A.A., Ensminger A.W., Qi P., Zucker J., Chess A. Monoallelic expression and asynchronous replication of p120 catenin in mouse and human cells. J Biol Chem 2005, 280:1354-1359.
7. Gimelbrant A., Hutchinson J.N., Thompson B.R., Chess A. Widespread monoallelic expression on human autosomes. Science 2007, 318:1136-1140.
8. Zwemer L.M., Zak A., Thompson B.R., Kirby A., Daly M.J., Chess A., Gimelbrant A.A. Autosomal monoallelic expression in the mouse. Genome Biol 2012, 13:R10.
9. Pernis B., Chiappino G., Kelus A.S., Gell P.G. Cellular localization of immunoglobulins with different allotypic specificities in rabbit lymphoid tissues. J Exp Med 1965, 122:853-876.
10. Chess A., Simon I., Cedar H., Axel R. Allelic inactivation regulates olfactory receptor gene expression. Cell 1994, 78:823-834.
11. Chess A. Random and non-random monoallelic expression. Neuropsychopharmacology 2013, 38:55-61.
12. Schlesinger S., Selig S., Bergman Y., Cedar H. Allelic inactivation of rDNA loci. Genes Dev 2009, 23:2437-2447.
13. Wang J., Valo Z., Smith D., Singer-Sam J. Monoallelic expression of multiple genes in the CNS. PLoS ONE 2007, 2:e1293.
14. Li S.M., Valo Z., Wang J., Gao H., Bowers C.W., Singer-Sam J. Transcriptome-wide survey of mouse CNS-derived cells reveals monoallelic expression within novel gene families. PLoS ONE 2012, 7:e31751.
15. Plenge R.M., Percec I., Nadeau J.H., Willard H.F. Expression-based assay of an X-linked gene to examine effects of the X-controlling element (Xce) locus. Mamm Genome 2000, 11:405-408.
16. Chadwick L.H., Pertz L.M., Broman K.W., Bartolomei M.S., Willard H.F. Genetic control of X chromosome inactivation in mice: definition of the Xce candidate interval. Genetics 2006, 173:2103-2110.
17. Heard E., Clerc P., Avner P. X-chromosome inactivation in mammals. Annu Rev Genet 1997, 31:571-610.
18. Chadwick L.H., Willard H.F. Genetic and parent-of-origin influences on X chromosome choice in Xce heterozygous mice. Mamm Genome 2005, 16:691-699.
19. Necsulea A., Semon M., Duret L., Hurst L.D. Monoallelic expression and tissue specificity are associated with high crossover rates. Trends Genet 2009, 25:519-522.
20. Gimelbrant A.A., Chess A. An epigenetic state associated with areas of gene duplication. Genome Res 2006, 16:723-729.
21. Jeffries A.R., Perfect L.W., Ledderose J., Schalkwyk L.C., Bray N.J., Mill J., Price J. Stochastic choice of allelic expression in human neural stem cells. Stem Cells 2012, 30:1938-1947.
22. Filippova G.N., Cheng M.K., Moore J.M., Truong J.P., Hu Y.J., Nguyen D.K., Tsuchiya K.D., Disteche C.M. Boundaries between chromosomal domains of X inactivation and escape bind CTCF and lack CpG methylation during early development. Dev Cell 2005, 8:31-42.
23. Calabrese J.M., Sun W., Song L., Mugford J.W., Williams L., Yee D., Starmer J., Mieczkowski P., Crawford G.E., Magnuson T. Site-specific silencing of regulatory elements as a mechanism of X inactivation. Cell 2012, 151:951-963.
24. Chow J.C., Ciaudo C., Fazzari M.J., Mise N., Servant N., Glass J.L., Attreed M., Avner P., Wutz A., Barillot E., et al. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 2010, 141:956-969.
25. Chaumeil J., Skok J.A. The role of CTCF in regulating V(D)J recombination. Curr Opin Immunol 2012, 24:153-159.
26. Nora E.P., Lajoie B.R., Schulz E.G., Giorgetti L., Okamoto I., Servant N., Piolot T., van Berkum N.L., Meisig J., Sedat J., et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012, 485:381-385.
27. Lomvardas S., Barnea G., Pisapia D.J., Mendelsohn M., Kirkland J., Axel R. Interchromosomal interactions and olfactory receptor choice. Cell 2006, 126:403-413.
28. Guo Y., Monahan K., Wu H., Gertz J., Varley K.E., Li W., Myers R.M., Maniatis T., Wu Q. CTCF/cohesin-mediated DNA looping is required for protocadherin alpha promoter choice. Proc Natl Acad Sci U S A 2012, 109:21081-21086.
29. Escamilla-Del-Arenal M., da Rocha S.T., Heard E. Evolutionary diversity and developmental regulation of X-chromosome inactivation. Hum Genet 2011, 130:307-327.
30. Lee J.T., Bartolomei M.S. X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 2013, 152:1308-1323.
31. Thayer M.J. Mammalian chromosomes contain cis-acting elements that control replication timing, mitotic condensation, and stability of entire chromosomes. Bioessays 2012, 34:760-770.
32. Pollex T., Heard E. Recent advances in X-chromosome inactivation research. Curr Opin Cell Biol 2012, 24:825-832.
33. Stoffregen E.P., Donley N., Stauffer D., Smith L., Thayer M.J. An autosomal locus that controls chromosome-wide replication timing and mono-allelic expression. Hum Mol Genet 2011, 20:2366-2378.
34. Donley N., Stoffregen E.P., Smith L., Montagna C., Thayer M.J. Asynchronous replication, mono-allelic expression, and long range cis-effects of ASAR6. PLoS Genet 2013, 9:e1003423.
35. Hellman A., Chess A. Gene body-specific methylation on the active X chromosome. Science 2007, 315:1141-1143.
36. Kerkel K., Spadola A., Yuan E., Kosek J., Jiang L., Hod E., Li K., Murty V.V., Schupf N., Vilain E., et al. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 2008, 40:904-908.
37. Wang J., Valo Z., Bowers C.W., Smith D.D., Liu Z., Singer-Sam J. Dual DNA methylation patterns in the CNS reveal developmentally poised chromatin and monoallelic expression of critical genes. PLoS ONE 2010, 5:e13843.
38. Brady B.L., Steinel N.C., Bassing C.H. Antigen receptor allelic exclusion: an update and reappraisal. J Immunol 2010, 185:3801-3808.
39. Mariani L., Schulz E.G., Lexberg M.H., Helmstetter C., Radbruch A., Lohning M., Hofer T. Short-term memory in gene induction reveals the regulatory principle behind stochastic IL-4 expression. Mol Syst Biol 2010, 6:359.
40. Kreso A., O'Brien C.A., van Galen P., Gan O., Notta F., Brown A.M., Ng K., Ma J., Wienholds E., Dunant C., et al. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science 2013, 339:543-548.
41. Sharma S.V., Lee D.Y., Li B., Quinlan M.P., Takahashi F., Maheswaran S., McDermott U., Azizian N., Zou L., Fischbach M.A., et al. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 2010, 141:69-80.
42. Zuo T., Wang L., Morrison C., Chang X., Zhang H., Li W., Liu Y., Wang Y., Liu X., Chan M.W., et al. FOXP3 is an X-linked breast cancer suppressor gene and an important repressor of the HER-2/ErbB2 oncogene. Cell 2007, 129:1275-1286.
43. Pereira J.P., Girard R., Chaby R., Cumano A., Vieira P. Monoallelic expression of the murine gene encoding Toll-like receptor 4. Nat Immunol 2003, 4:464-470.
44. Quon K.C., Berns A. Haplo-insufficiency? Let me count the ways. Genes Dev 2001, 29:7-2921.
45. Kirchgessner C.U., Warren S.T., Willard H.F. X inactivation of the FMR1 fragile X mental retardation gene. J Med Genet 1995, 32:925-929.
46. Amir R.E., Van den Veyver I.B., Schultz R., Malicki D.M., Tran C.Q., Dahle E.J., Philippi A., Timar L., Percy A.K., Motil K.J., et al. Influence of mutation type and X chromosome inactivation on Rett syndrome phenotypes. Ann Neurol 2000, 47:670-679.
47. Young J.I., Zoghbi H.Y. X-chromosome inactivation patterns are unbalanced and affect the phenotypic outcome in a mouse model of Rett syndrome. Am J Hum Genet 2004, 74:511-520.
48. Huang H.S., Allen J.A., Mabb A.M., King I.F., Miriyala J., Taylor-Blake B., Sciaky N., Dutton J.W., Lee H.M., Chen X., et al. Topoisomerase inhibitors unsilence the dormant allele of Ube3a in neurons. Nature 2012, 481:185-189.
49. Berger A.H., Knudson A.G., Pandolfi P.P. A continuum model for tumour suppression. Nature 2011, 476:163-169.
50. Morey C., Avner P. The demoiselle of X-inactivation: 50 years old and as trendy and mesmerising as ever. PLoS Genet 2011, 7:e1002212.
51. Pinter S.F., Sadreyev R.I., Yildirim E., Jeon Y., Ohsumi T.K., Borowsky M., Lee J.T. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. Genome Res 2012, 22:1864-1876.
52. Fuss S.H., Omura M., Mombaerts P. Local and cis effects of the H element on expression of odorant receptor genes in mouse. Cell 2007, 130:373-384.
53. Singh N., Ebrahimi F.A., Gimelbrant A.A., Ensminger A.W., Tackett M.R., Qi P., Gribnau J., Chess A. Coordination of the random asynchronous replication of autosomal loci. Nat Genet 2003, 33:339-341.
54. Clowney E.J., LeGros M.A., Mosley C.P., Clowney F.G., Markenskoff-Papadimitriou E.C., Myllys M., Barnea G., Larabell C.A., Lomvardas S. Nuclear aggregation of olfactory receptor genes governs their monogenic expression. Cell 2012, 151:724-737.
55. Magklara A., Yen A., Colquitt B.M., Clowney E.J., Allen W., Markenscoff-Papadimitriou E., Evans Z.A., Kheradpour P., Mountoufaris G., Carey C., et al. An epigenetic signature for monoallelic olfactory receptor expression. Cell 2011, 145:555-570.
56. Vettermann C., Schlissel M.S. Allelic exclusion of immunoglobulin genes: models and mechanisms. Immunol Rev 2010, 237:22-42.
57. Farago M., Rosenbluh C., Tevlin M., Fraenkel S., Schlesinger S., Masika H., Gouzman M., Teng G., Schatz D., Rais Y., et al. Clonal allelic predetermination of immunoglobulin-kappa rearrangement. Nature 2012, 490:561-565.
58. Weiner J.A., Jontes J.D. Protocadherins, not prototypical: a complex tale of their interactions, expression, and functions. Front Mol Neurosci 2013, 6:4.