Interrogating the transcriptome of oocytes and preimplantation embryos

Methods in Enzymology

Volumn 477, Issue C, 2010, Pages 481-510

  Peaston, Anne E ^a   Graber, Joel H ^a   Knowles, Barbara B ^b   de Vries, Wilhelmine N ^a  

^a JACKSON LABORATORY   (United States)

^b INSTITUTE OF MEDICAL BIOLOGY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSCRIPTOME;

ANIMAL CELL; ARTICLE; CELL GROWTH; FEMALE; GENETIC TRANSCRIPTION; MOUSE; NONHUMAN; OOCYTE; POLYADENYLATION; PREIMPLANTATION EMBRYO; PRIORITY JOURNAL; PROTEIN SYNTHESIS; RNA DEGRADATION; RNA TRANSLATION; SYSTEMATIC ERROR; TRANSCRIPTION INITIATION;

EID: 77955368194     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)77024-5     Document Type: Chapter

References (66)

1. Anonymous Application Note SOLiD™ System High-Throughput Analysis of Differential Gene Expression. Applied Biosystems 2008, Foster City, CA, USA.
2. Bachvarova R. Incorporation of tritiated adenosine into mouse ovum RNA. Dev. Biol. 1974, 40:52-58.
3. Bachvarova R. Gene expression during oogenesis and oocyte development in mammals. Developmental Biology a Comprehensive Synthesis, Oogenesis 1985, 453. Plenum Press, New York. L.W. Browder (Ed.).
4. Bachvarova R.F. A maternal tail of poly(A): The long and the short of it. Cell 1992, 69:895-897.
5. Bachvarova R., De Leon V. Polyadenylated RNA of mouse ova and loss of maternal RNA in early development. Dev. Biol. 1980, 74:1-8.
6. Bachvarova R., De Leon V., Johnson A., Kaplan G., Paynton B.V. Changes in total RNA, polyadenylated RNA, and actin mRNA during meiotic maturation of mouse oocytes. Dev. Biol. 1985, 108:325-331.
7. Baker P.J., O'Shaughnessy P.J. Expression of prostaglandin D synthetase during development in the mouse testis. Reproduction 2001, 122:553-559.
8. Baugh L.R., Hill A.A., Brown E.L., Hunter C.P. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res. 2001, 29:E29.
9. Belloc E., Pique M., Mendez R. Sequential waves of polyadenylation and deadenylation define a translation circuit that drives meiotic progression. Biochem. Soc. Trans. 2008, 36:665-670.
10. Brady G., Iscove N.N. Construction of cDNA libraries from single cells. Methods Enzymol. 1993, 225:611-623.
11. Brower P.T., Gizang E., Boreen S.M., Schultz R.M. Biochemical studies of mammalian oogenesis: Synthesis and stability of various classes of RNA during growth of the mouse oocyte in vitro. Dev. Biol. 1981, 86:373-383.
12. Clegg K.B., Piko L. Poly(A) length, cytoplasmic adenylation and synthesis of poly(A)+RNA in early mouse embryos. Dev. Biol. 1983, 95:331-341.
13. Clegg K.B., Piko L. Quantitative aspects of RNA synthesis and polyadenylation in 1-cell and 2-cell mouse embryos. J. Embryol. Exp. Morphol. 1983, 74:169-182.
14. Dai M., Wang P., Boyd A.D., Kostov G., Athey B., Jones E.G., Bunney W.E., Myers R.M., Speed T.P., Akil H., Watson S.J., Meng F. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 2005, 33(20):e175.
15. De Leon V., Johnson A., Bachvarova R. Half-lives and relative amounts of stored and polysomal ribosomes and poly(A) + RNA in mouse oocytes. Dev. Biol. 1983, 98:400-408.
16. Evsikov A.V., Marin de Evsikova C. Evolutionary origin and phylogenetic analysis of the novel oocyte-specific eukaryotic translation initiation factor 4E in Tetrapoda. Dev. Genes Evol. 2009, 219:111-118.
17. Evsikov A.V., Marin de Evsikova C. Gene expression during the oocyte-to-embryo transition in mammals. Mol. Reprod. Dev. 2009, 76:805-818.
18. Evsikov A.V., de Vries W.N., Peaston A.E., Radford E.E., Fancher K.S., Chen F.H., Blake J.A., Bult C.J., Latham K.E., Solter D., Knowles B.B. Systems biology of the 2-cell mouse embryo. Cytogenet. Genome Res. 2004, 105:240-250.
19. Evsikov A.V., Graber J.H., Brockman J.M., Hampl A., Holbrook A.E., Singh P., Eppig J.J., Solter D., Knowles B.B. Cracking the egg: Molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo. Genes Dev. 2006, 20:2713-2727.
20. Faulkner G.J., Kimura Y., Daub C.O., Wani S., Plessy C., Irvine K.M., Schroder K., Cloonan N., Steptoe A.L., Lassmann T., Waki K., Hornig N., et al. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 2009, 41:563-571.
21. Gautier L., Cope L., Bolstad B.M., Irizarry R.A. Affy-Analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315.
22. Gebauer F., Xu W., Cooper G.M., Richter J.D. Translational control by cytoplasmic polyadenylation of c-mos mRNA is necessary for oocyte maturation in the mouse. EMBO J. 1994, 13:5712-5720.
23. Hamatani T., Carter M.G., Sharov A.A., Ko M.S. Dynamics of global gene expression changes during mouse preimplantation development. Dev. Cell 2004, 6:117-131.
24. Harwood B.N., Cross S.K., Radford E.E., Haac B.E., De Vries W.N. Members of the WNT signaling pathways are widely expressed in mouse ovaries, oocytes, and cleavage stage embryos. Dev. Dyn. 2008, 237:1099-1111.
25. Huarte J., Belin D., Vassalli A., Strickland S., Vassalli J.D. Meiotic maturation of mouse oocytes triggers the translation and polyadenylation of dormant tissue-type plasminogen activator mRNA. Genes Dev. 1987, 1:1201-1211.
26. Hwang S., Benjamin L.E., Oh B., Rothstein J.L., Ackerman S.L., Beddington R.S., Solter D., Knowles B.B. Genetic mapping and embryonic expression of a novel, maternally transcribed gene Mem3. Mamm. Genome 1996, 7:586-590.
27. Hwang S.Y., Oh B., Fuchtbauer A., Fuchtbauer E.M., Johnson K.R., Solter D., Knowles B.B. Maid: A maternally transcribed novel gene encoding a potential negative regulator of bHLH proteins in the mouse egg and zygote. Dev. Dyn. 1997, 209:217-226.
28. Hwang S.Y., Oh B., Zhang Z., Miller W., Solter D., Knowles B.B. The mouse cornichon gene family. Dev. Genes Evol. 1999, 209:120-125.
29. Iscove N.N., Barbara M., Gu M., Gibson M., Modi C., Winegarden N. Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat. Biotechnol. 2002, 20:940-943.
30. Ji W., Zhou W., Gregg K., Lindpaintner K., Davis S. A method for gene expression analysis by oligonucleotide arrays from minute biological materials. Anal. Biochem. 2004, 331:329-339.
31. Kaplan G., Abreu S.L., Bachvarova R. rRNA accumulation and protein synthetic patterns in growing mouse oocytes. J. Exp. Zool. 1982, 220:361-370. (calculated from ribosomal RNA content), quoted in Bachvarova (1985).
32. Klur S., Toy K., Williams M.P., Certa U. Evaluation of procedures for amplification of small-size samples for hybridization on microarrays. Genomics 2004, 83:508-517.
33. Ko M.S., Kitchen J.R., Wang X., Threat T.A., Hasegawa A., Sun T., Grahovac M.J., Kargul G.J., Lim M.K., Cui Y., Sano Y., Tanaka T., et al. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Development 2000, 127:1737-1749.
34. Lang J.E., Magbanua M.J., Scott J.H., Makrigiorgos G.M., Wang G., Federman S., Esserman L.J., Park J.W., Haqq C.M. A comparison of RNA amplification techniques at sub-nanogram input concentration. BMC Genomics 2009, 10:326.
35. Lequarre A.S., Traverso J.M., Marchandise J., Donnay I. Poly(A) RNA is reduced by half during bovine oocyte maturation but increases when meiotic arrest is maintained with CDK inhibitors. Biol. Reprod. 2004, 71:425-431.
36. Li C., Hung Wong W. Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application. Genome Biol. 2001, 2. RESEARCH0032.1-RESEARCH0032.11.
37. Mamo S., Gal A.B., Bodo S., Dinnyes A. Quantitative evaluation and selection of reference genes in mouse oocytes and embryos cultured in vivo and in vitro. BMC Dev. Biol. 2007, 7:14.
38. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5:621-628.
39. Murchison E.P., Stein P., Xuan Z., Pan H., Zhang M.Q., Schultz R.M., Hannon G.J. Critical roles for Dicer in the female germline. Genes Dev. 2007, 21:682-693.
40. Manipulating the Mouse Embryo a Laboratory Manual 2003, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. A. Nagy, M. Gertsenstein, K. Vintersten, R. Behringer (Eds.).
41. Oh B., Hwang S.Y., Solter D., Knowles B.B. Spindlin, a major maternal transcript expressed in the mouse during the transition from oocyte to embryo. Development 1997, 124:493-503.
42. Oh B., Hwang S., McLaughlin J., Solter D., Knowles B.B. Timely translation during the mouse oocyte-to-embryo transition. Development 2000, 127:3795-3803.
43. Olds P.J., Stern S., Biggers J.D. Chemical estimates of the RNA and DNA contents of the early mouse embryo. J. Exp. Zool. 1973, 186:39-46.
44. Paynton B.V., Rempel R., Bachvarova R. Changes in state of adenylation and time course of degradation of maternal mRNAs during oocyte maturation and early embryonic development in the mouse. Dev. Biol. 1988, 129:304-314.
45. Peaston A.E., Evsikov A.V., Graber J.H., de Vries W.N., Holbrook A.E., Solter D., Knowles B.B. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 2004, 7:597-606.
46. Piko L., Clegg K.B. Quantitative changes in total RNA, total poly(A), and ribosomes in early mouse embryos. Dev. Biol. 1982, 89:362-378.
47. Pique M., Lopez J.M., Foissac S., Guigo R., Mendez R. A combinatorial code for CPE-mediated translational control. Cell 2008, 132:434-448.
48. Pirooznia M., Nagarajan V., Deng Y. GeneVenn-A web application for comparing gene lists using Venn diagrams. Bioinformation 2007, 1:420-422.
49. Rambhatla L., Patel B., Dhanasekaran N., Latham K.E. Analysis of G protein alpha subunit mRNA abundance in preimplantation mouse embryos using a rapid, quantitative RT-PCR approach. Mol. Reprod. Dev. 1995, 41:314-324.
50. Rothstein J.L., Johnson D., DeLoia J.A., Skowronski J., Solter D., Knowles B. Gene expression during preimplantation mouse development. Genes Dev. 1992, 6:1190-1201.
51. Rothstein J.L., Johnson D., Jessee J., Skowronski J., DeLoia J.A., Solter D., Knowles B.B. Construction of primary and subtracted cDNA libraries from early embryos. Methods Enzymol. 1993, 225:587-610.
52. Salisbury J., Hutchison K.W., Wigglesworth K., Eppig J.J., Graber J.H. Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation. PLoS One 2009, 4:e7479.
53. Sharov A.A., Piao Y., Matoba R., Dudekula D.B., Qian Y., VanBuren V., Falco G., Martin P.R., Stagg C.A., Bassey U.C., Wang Y., Carter M.G., et al. Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol. 2003, 1:E74.
54. Stahlberg A., Hakansson J., Xian X., Semb H., Kubista M. Properties of the reverse transcription reaction in mRNA quantification. Clin. Chem. 2004, 50:509-515.
55. Stangegaard M., Dufva I.H., Dufva M. Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA. Biotechniques 2006, 40:649-657.
56. Sternlicht A.L., Schultz R.M. Biochemical studies of mammalian oogenesis: Kinetics of accumulation of total and poly(A)-containing RNA during growth of the mouse oocyte. J. Exp. Zool. 1981, 215:191-200.
57. Su Y.Q., Sugiura K., Woo Y., Wigglesworth K., Kamdar S., Affourtit J., Eppig J.J. Selective degradation of transcripts during meiotic maturation of mouse oocytes. Dev. Biol. 2007, 302:104-117.
58. Subkhankulova T., Livesey F.J. Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level. Genome Biol. 2006, 7:R18.
59. Tam O.H., Aravin A.A., Stein P., Girard A., Murchison E.P., Cheloufi S., Hodges E., Anger M., Sachidanandam R., Schultz R.M., Hannon G.J. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 2008, 453:534-538.
60. Tanaka T.S., Jaradat S.A., Lim M.K., Kargul G.J., Wang X., Grahovac M.J., Pantano S., Sano Y., Piao Y., Nagaraja R., Doi H., Wood W.H., et al. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Proc. Natl. Acad. Sci. USA 2000, 97:9127-9132.
61. Tang F., Barbacioru C., Wang Y., Nordman E., Lee C., Xu N., Wang X., Bodeau J., Tuch B.B., Siddiqui A., Lao K., Surani M.A. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 2009, 6:377-382.
62. Van Gelder R.N., von Zastrow M.E., Yool A., Dement W.C., Barchas J.D., Eberwine J.H. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. USA 1990, 87:1663-1667.
63. Wang Q.T., Piotrowska K., Ciemerych M.A., Milenkovic L., Scott M.P., Davis R.W., Zernicka-Goetz M. A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Dev. Cell 2004, 6:133-144.
64. Watanabe T., Totoki Y., Toyoda A., Kaneda M., Kuramochi-Miyagawa S., Obata Y., Chiba H., Kohara Y., Kono T., Nakano T., Surani M.A., Sakaki Y., et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 2008, 453:539-543.
65. West M.F., Verrotti A.C., Salles F.J., Tsirka S.E., Strickland S. Isolation and characterization of two novel, cytoplasmically polyadenylated, oocyte-specific, mouse maternal RNAs. Dev. Biol. 1996, 175:132-141.
66. Zeng F., Schultz R.M. Gene expression in mouse oocytes and preimplantation embryos: Use of suppression subtractive hybridization to identify oocyte- and embryo-specific genes. Biol. Reprod. 2003, 68:31-39.