Determination of microRNAs in mouse preimplantation embryos by microarray

Developmental Dynamics

Volumn 237, Issue 9, 2008, Pages 2315-2327

  Yang, Yanhong ^a   Bai, Wentao ^b   Zhang, Liang ^c   Yin, Guowu ^a   Wang, Xiaohong ^a   Wang, Jun ^a   Zhao, Hongxi ^a   Han, Yibing ^d   Yao, Yuan Qing ^a,e  

^a FOURTH MILITARY MEDICAL UNIVERSITY   (China)

^b FOURTH MILITARY MEDICAL UNIVERSITY   (China)

^c NATIONAL ENGINEERING RESEARCH CENTER FOR BEIJING BIOCHIP TECHNOLOGY   (China)

^d CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^e CHINESE PLA GENERAL HOSPITAL   (China)

Author keywords

Microarray; miRNA; Preimplantation embryos

Indexed keywords

MICRORNA;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CLASSIFICATION; CONTROL GROUP; CONTROLLED STUDY; DEVELOPMENTAL STAGE; EMBRYO; FEMALE; GENE EXPRESSION; GENE TARGETING; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; OOCYTE; PREIMPLANTATION EMBRYO; PRIORITY JOURNAL; PROCESS DEVELOPMENT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA DEGRADATION;

ANIMALS; BLASTOCYST; FEMALE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MICE; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 51549086927     PISSN: 10588388     EISSN: 10970177     Source Type: Journal    
DOI: 10.1002/dvdy.21666     Document Type: Article

References (58)

1. Alizadeh Z, Kageyama S, Aoki F. 2005. Degradation of maternal mRNA in mouse embryos: selective degradation of specific mRNAs after fertilization. Mol Reprod Dev 72:281-290.
2. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H. 2005. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 33:2697-2706.
3. Amanai M, Brahmajosyula M, Perry ACF. 2006. A restricted role for sperm-borne microRNAs in mammalian fertilization. Biol Reprod 75:877-884.
4. Ambros C. 2004. The functions of animal microRNAs. Nature 431:350-355.
5. Bachvarova R, De Leon C, Johnson A, Kaplan G, Paynton BV. 1985. Changes in total RNA, polyadenylated RNA, and actin mRNA during meiotic maturation of mouse oocytes. Dev Biol 108:325-331.
6. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE. 2005. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122:553-563.
7. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297.
8. Chen K, Rajewsky N. 2007. The evolution of gene regulation by transcriptional factors and miRNAs. Nature 8:93-103.
9. Cui XS, Shen SH, Kim NH. 2007a. Dicer1 expression in preimplantation mouse embryos: involvement of Oct3/4 transcription at the blastocyst stage. Biochem Biophys Res Commun 352:231-236.
10. Cui XS, Li XY, Yin XJ, Kong IK, Kang JJ, Kim NH. 2007b. Maternal gene transcription in mouse oocytes: genes implicated in oocyte maturation and fertilization. J Reprod Dev 53:405-418.
11. Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O, Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H, Kinzler KW, Vogelstein B, Velculescu VE. 2006. The colorectal microRNAome. Proc Natl Acad Sci U S A 103:3687-3692.
12. Dard N, Louvet-Vallee S, Santa-Maria A, Maro B. 2004. Phosphorylation of ezrin on threonine T567 plays a crucial role during compaction in the mouse early embryo. Dev Biol 271:87-97.
13. Du T, Zamore PD. 2005. MicroPrimer: the biogenesis and function of microRNA. Development 132:4645-4652.
14. Eis PS, Tam W, Sun L, Chadburn A, Li Z, Gomez MF, Lund E, Dahlberg JE. 2005. Accumulation of miR-155 and BIC RNA in human B cell in lymphomas. Proc Natl Acad Sci U S A 102:3624-3632.
15. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95:14863-14868.
16. Evsikov AV, Graber JH, Brockman JM, Hampl A, Holbrook AE, Singh P, Eppig JJ, Solter D, Knowles BB. 2006. Cracking the egg: molecular dynamics and evolutionary aspects of the transition from fully grown oocyte to embryo. Genes Dev 20:2713-2727.
17. Flemming TP, Johnson MH. 1988. From egg to epithelium. Annu Rev Cell Biol 4:459-485.
18. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Dongen SC, Inoue K, Enright AJ, Schier AF. 2006. Zabrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312:75-79.
19. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. 2007. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27:91-105.
20. Haase AD, Jaskiewics L, Zhang H, Laines S, Sack R, Gatignol A, Filipowicz W. 2005. TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep 6:961-967.
21. Hamatani T, Carter MG, Sharov AA, Ko MS. 2004. Dynamics of global gene expression changes during mouse preimplantation development. Dev Cell 6:117-131.
22. He L, Hannon GJ. 2004. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5:522-531.
23. Houbaviy HB, Murray MF, Sharp PA. 2003. Embryonic stem cell-specific micro-RNAs. Dev Cell 5:351-358.
24. Hyafil F, Babinet C, Jacob F. 1981. Cell-cell interactions in early embryogenesis: a molecular approach to the role of calcium. Cell 26:447-454.
25. Jing Q, Huang S, Guth S, Zarubin T, Motoyama A, Chen J, Di Padova F, Lin SC, Gram H, Han J. 2005. Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 120:623-634.
26. Lagos-Quintana M, Rauhut R, Yalcin A Meyer J, Lendeckel W, Tuschl T. 2002. Identification of tissue-specific microRNAs from mouse. Curr Biol 12:735-739.
27. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T. 2007. A mammalian micorRNA expression atlas based on small RNA library sequencing. Cell 129:1401-1414.
28. Li XY, Cui XS, Kim NH. 2006. Transcription profile during maternal to zygotic transition in the mouse embryo. Reprod Fertil Dev 18:635-645.
29. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. 2003. Vertebrate microRNA genes. Science 299:1540.
30. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsely PS, Johnson JM. 2005. Microarray analysis shows that some microRNAs down-regulate large numbers of target mRNAs. Nature 433:769-773.
31. Lui Wo, Pourmand N, Patterson BK, Fire A. 2007. Patterns of known and novel small RNAs in human cervical cancer. Cancer Res 67:6031-6043.
32. Luo M, Tian Z, Xu Z, Zhang L, Wang Y, Cheng J. 2007. Construction and application of a microarray for profiling miRNA expression. Prog Biochem Biophys 34:31-41.
33. Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K, Mirochnitchenko O, Inouye M, Kato I. 2006. The expression profile of miRNAs in mouse embryos. Nucleic Acid Res 34:1765-1771.
34. Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, Hannon G. 2007. Critical roles for Dicer in the female germline. Genes Dev 21:682-693.
35. Nakahara K, Kim K, Sciulli C, Dowd SR, Minden JS, Carthew RW. 2005. Targets of microRNA regulation in the Drosophila oocyte preteome. Proc Natl Acad Sci U S A 102:12023-12038.
36. Nothiase JY, Majumder S, Kaneko KJ, DePamphilis ML. 1995. Regulation of gene expression at the beginning of mammalian development. J Biol Chem 270:22077-22080.
37. Patterson TA, Lobenhofer EK, Fulmer-Smentek B, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ, Zhang L, Hurban P, de Longueville F, Fuscoe JC, Tong W, Shi L, Wolfinger RD. 2006. Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project. Nat Biotechnol 24:1140-1150.
38. Paynton BV, Remple D, Bachvarova R. 1988. 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 129:304-314.
39. Pfaffl MW. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45.
40. Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M. 2004. Pancreatic islet-specific mircroRNA regulates insulin secretion. Nature 432:226-230.
41. Rajewsky N. 2006. MicroRNA target predictions in animals. Nature Genetics Supplement 38:s8-s13.
42. Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M. 2005. Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 6:267-281.
43. Schultz RM. 2002. The molecular foundations of the maternal to zygotic transition in the preimplantation embryo. Hum Reprod Update 8:323-331.
44. Stanton JL, Green DPL. 2001. Meta-analysis of gene expression in mouse preimplantation embryo development. Mol Hum Reprod 7:545-552.
45. Stanton JA, Macgregor AB, Mason C, Dameh M, Green DP. 2007. Building comparative gene expression databases for the mouse preimplantation embryo using a pipeline approach to UniGene. Mol Hum Reprod 13:713-720.
46. Sood P, Krek A, Zavolan M, Macino G, Rajewsky N. 2006. Cell-type-specific signatures of miRNAs on target mRNA expression. Proc Natl Acad Sci U S A 8:2746-2751.
47. Sudheer S, Adjaye J. 2007. Functional genomics of human pre-implantation development. Brief Funct Genomic Proteomic 6:120-132.
48. Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS, Moon SY, Kim VN, Kim KS. 2004. Human embryonic stem cells express a unique set of microRNAs. Dev Biol 270:488-498.
49. Tang F, Kaneda M, O'Carrol D, Hajkova P, Barton SC, Sun YA, Lee C, Tarakhovsky A, Lao K, Surani MA. 2007. Maternal microRNAs are essential for mouse zygotic development. Gene Dev 21:644-648.
50. Thomson JM, Parker J, Perou CM, Hammond SM. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat Methods 1:47-53.
51. Tichopad A, Dilger M, Schwarz G, Pfaffl MW. 2003. Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Res 31:e122.
52. Wang QT, Piotrowska K, Ciemerych MA, Milenkovic L, Scott MP, Davis RW, Zernicka-Goetx M. 2004. A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryos. Dev Cell 6:133-144.
53. Watanabe T, Takeda A, Mise K, Okuno T, Suzuki T, Minami N, Imai H. 2005. Stage-specific expression of microRNAs during Xenopus development. FEBS Lett 579:318-324.
54. Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H. 2006. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev 20:1732-1743.
55. Wheeler G, Ntounia-Fousara S, Granda B, Rathjen T, Dalmay T. 2006. Identification of new central nervous system specific mouse microRNAs. FEBS Lett 580:2195-2200.
56. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. 2005. Systematic discovery of regulatory motifs in human promoters and 3′UTRs by comparison of several mammals. Nature 434:338-345.
57. Yu Z, Jian Z, Shen SH, Purisima E, Wang E. 2007. Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic Acids Res 35:152-164.
58. Zeng F, Baldwin DA, Schultz RM. 2004. Transcript profiling during preimplantation mouse development. Dev Biol 272:483-496.