Deterministic and stochastic allele specific gene expression in single mouse blastomeres

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Tang, Fuchou ^a,c   Barbacioru, Catalin ^b   Nordman, Ellen ^b   Bao, Siqin ^a   Lee, Caroline ^a   Wang, Xiaohui ^b   Tuch, Brian B ^b   Heard, Edith ^d   Lao, Kaiqin ^b   Surani, M Azim ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b APPLIED BIOSYSTEMS   (United States)

^c PEKING UNIVERSITY   (China)

^d INSTITUT CURIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTOME; UNTRANSLATED RNA; ISOPROTEIN;

3' UNTRANSLATED REGION; ALLELE; ALLELE SPECIFIC GENE EXPRESSION; ALLELIC IMBALANCE; ANIMAL CELL; ARTICLE; BLASTOMERE; CELL SPECIFICITY; CONTROLLED STUDY; DEVELOPMENTAL GENETICS; EMBRYO; EMBRYO DEVELOPMENT; FALSE POSITIVE RESULT; FEMALE; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENE LOCUS; MOUSE; NONHUMAN; OOCYTE; PHENOTYPE; PREIMPLANTATION EMBRYO; RNA SEQUENCE; RNA SPLICING; TRANSCRIPTION REGULATION; ALTERNATIVE RNA SPLICING; ANIMAL; BLASTOCYST; CYTOLOGY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; PRINCIPAL COMPONENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICS;

3' UNTRANSLATED REGIONS; ALLELES; ALLELIC IMBALANCE; ALTERNATIVE SPLICING; ANIMALS; BLASTOCYST; BLASTOMERES; EMBRYONIC DEVELOPMENT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MICE; MICRORNAS; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; PROTEIN ISOFORMS; RNA, UNTRANSLATED; STOCHASTIC PROCESSES;

EID: 79959567069     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021208     Document Type: Article

References (48)

1. Rossant J, Tam PP, (2009) Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse. Development 136: 701-713.
2. Cheung VG, Spielman RS, (2002) The genetics of variation in gene expression. Nat Genet 32: S522-S525.
3. Cheung VG, Bruzel A, Burdick JT, Morley M, Devlin JL, et al. (2008) Monozygotic twins reveal germline contribution to allelic expression differences. Am J Hum Genet 82: 1357-1360.
4. Chow J, Heard E, (2009) X inactivation and the complexities of silencing a sex chromosome. Curr Opin Cell Biol 21: 359-366.
5. Ferguson-Smith AC, Surani MA, (2001) Imprinting and the epigenetic asymmetry between parental genomes. Science 293: 1086-1089.
6. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
7. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
8. Alimonti A, Carracedo A, Clohessy JG, Trotman LC, Nardella C, et al. (2010) Subtle variations in Pten dose determine cancer susceptibility. Nat Genet 42: 454-458.
9. 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: 643-648.
10. Gregg C, Zhang J, Butler JE, Haig D, Dulac C, (2010) Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329: 682-685.
11. McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, et al. (2010) Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328: 235-239.
12. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The diploid genome sequence of an individual human. PLoS Biol 5: e254.
13. Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW, (2002) Allelic variation in human gene expression. Science 297: 1143.
14. Zhang K, Li JB, Gao Y, Egli D, Xie B, et al. (2009) Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods 6: 613.
15. Pant PV, Tao H, Beilharz EJ, Ballinger DG, Cox DR, et al. (2006) Analysis of allelic differential expression in human white blood cells. Genome Res 16: 331-339.
16. Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA, et al. (2008) SNP-specific array-based allele-specific expression analysis. Genome Res 18: 771-779.
17. Gagneur J, Sinha H, Perocchi F, Bourgon R, Huber W, et al. (2009) Genome-wide allele- and strand-specific expression profiling. Mol Syst Biol 5: 274.
18. Main BJ, Bickel RD, McIntyre LM, Graze RM, Calabrese PP, et al. (2009) Allele-specific expression assays using Solexa. BMC Genomics 10: 422.
19. Palacios R, Gazave E, Goñi J, Piedrafita G, Fernando O, et al. (2009) Allele-specific gene expression is widespread across the genome and biological processes. PLoS One 4: e4150.
20. 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: 122-134.
21. Daelemans C, Ritchie ME, Smits G, Abu-Amero S, Sudbery IM, et al. (2010) High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. BMC Genet 11: 25.
22. Arias AM, Hayward P, (2006) Filtering transcriptional noise during development: concepts and mechanisms. Nat. Rev. Genet 7: 34-44.
23. Raj A, van Oudenaarden A, (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135: 216-226.
24. Huang S, (2009) Non-genetic heterogeneity of cells in development: more than just noise. Development 136: 3853-3862.
25. Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S, (2008) Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453: 544-547.
26. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S, (2006) Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4: e309.
27. Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, et al. (2008) Dynamic proteomics of individual cancer cells in response to a drug. Science 322: 1511-1516.
28. Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, et al. (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533-538.
29. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, et al. (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6: 377-382.
30. Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, et al. (2003) Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol 1: E74.
31. Hamatani T, Carter MG, Sharov AA, Ko MS, (2004) Dynamics of global gene expression changes during mouse preimplantation development. Dev Cell 6: 117-131.
32. Wang QT, Piotrowska K, Ciemerych MA, Milenkovic L, Scott MP, et al. (2004) A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Dev Cell 6: 133-144.
33. Bell CE, Calder MD, Watson AJ, (2008) Genomic RNA profiling and the programme controlling preimplantation mammalian development. Mol Hum Reprod 14: 691-701.
34. O'Neill MJ, (2005) The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum Mol Genet 14: R113-R120.
35. Kadota M, Yang HH, Hu N, Wang C, Hu Y, et al. (2007) Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome. PLoS Genet 3: e81.
36. Schalkwyk LC, Meaburn EL, Smith R, Dempster EL, Jeffries AR, et al. (2010) Allelic skewing of DNA methylation is widespread across the genome. Am J Hum Genet 86: 196-212.
37. Chen M, Manley, L J, (2009) Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 10: 741-754.
38. Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB, (2008) Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320: 1643-1647.
39. Mayr C, Bartel DP, (2009) Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138: 673-684.
40. Ji Z, Tian B, (2009) Reprogramming of 3′ untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS One 4: e8419.
41. Ji Z, Lee JY, Pan Z, Jiang B, Tian B, (2009) Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A 106: 7028-7033.
42. Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
43. Fu X, Fu N, Guo S, Yan Z, Xu Y, et al. (2009) Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 10: 161.
44. Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM, (2005) Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell 123: 1133-1146.
45. Nagy A, Gertsenstein M, Vintersten K, Behringer R, (2003) Recovery and in vitro culture of preimplantation stage embryos. In: Manipulating the Mouse Embryo 3rd edn 194-200 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York).
46. Tang F, Barbacioru C, Bao S, Lee C, Nordman E, et al. (2010) Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell 6: 468-478.
47. Tang F, Barbacioru C, Nordman E, Li B, Xu N, et al. (2010) RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5: 516-535.
48. Tuch BB, Laborde RR, Xu X, Gu J, Chung CB, et al. (2010) Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations. PLoS One 5: e9317.