Gene trap as a tool for genome annotation and analysis of X chromosome inactivation in human embryonic stem cells

Nucleic Acids Research

Volumn 32, Issue 13, 2004, Pages 3995-4002

  Dhara, Sujoy K ^a   Benvenisty, Nissim ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

HISTIDINE TRANSFER RNA LIGASE; PHOSPHOPROTEIN PHOSPHATASE 1; PLECKSTRIN; PROTEIN TYROSINE PHOSPHATASE;

ARTICLE; CELL DIFFERENTIATION; CHROMOSOME ANALYSIS; CHROMOSOME INSERTION; CHROMOSOME SIZE; CONTROLLED STUDY; EMBRYO; EMBRYO CELL; EMBRYO DEVELOPMENT; GENE EXPRESSION; GENE INSERTION; GENE MUTATION; GENETIC IDENTIFICATION; GENETIC MANIPULATION; GENETIC SELECTION; GENOME ANALYSIS; HUMAN; HUMAN CELL; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; STEM CELL; X CHROMOSOME INACTIVATION; ANIMAL; CELL CLONE; CELL CULTURE; CYTOLOGY; FEMALE; GENE EXPRESSION REGULATION; GENOME; METABOLISM; METHODOLOGY; MOUSE; X CHROMOSOME;

INSERTION SEQUENCES;

ANIMALS; CELL DIFFERENTIATION; CELLS, CULTURED; CLONE CELLS; EMBRYO; FEMALE; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; MICE; MUTAGENESIS, INSERTIONAL; STEM CELLS; X CHROMOSOME;

EID: 3242791094     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh746     Document Type: Article

References (32)

1. Thomson,J.A., Itskovitz-Eldor,J., Shapiro,S.S., Waknitz,M.A., Swiergiel,J.J., Marshall,V.S. and Jones,J.M. (1998) Embryonic stem cell lines derived from human blastocysts. Science, 282, 1145-1147.
2. Reubinoff,B.E., Pera,M.F., Fong,C.Y., Trounson,A. and Bongso,A. (2000) Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro. Nat. Biotechnol., 18, 399-404.
3. Itskovitz-Eldor,J., Schuldiner,M., Karsenti,D., Eden,A., Yanuka,O., Amit,M., Soreq,H. and Benvenisty,N. (2000) Differentiation of human embryonic stem cells into embryoid bodies compromising the three embryonic germ layers. Mol. Med., 6, 88-95.
4. Schuldiner,M., Yanuka,O., Itskovitz-Eldor,J., Melton,D.A. and Benvenisty,N. (2000) Effects of eight growth factors on the differentiation of cells derived from human embryonic stem cells. Proc. Natl Acad. Sci. USA, 97, 11307-11312.
5. Eiges,R., Schuldiner,M., Drukker,M., Yanuka,O., Itskovitz-Eldor,J. and Benvenisty,N. (2001) Establishment of human embryonic stem cell-transfected clones carrying a marker for undifferentiated cells. Curr. Biol., 11, 514-518.
6. Schuldiner,M., Itskovitz-Eldor,J. and Benvenisty,N. (2003) Selective ablation of human embryonic stem cells expressing a 'suicide' gene. Stem Cells, 21, 257-265.
7. Henderson,J.K., Draper,J.S., Baillie,H.S., Fishel,S., Thomson,J.A., Moore,H. and Andrews,P.W. (2002) Preimplantation human embryos and embryonic stem cells show comparable expression of stage-specific embryonic antigens. Stem Cells, 20, 329-337.
8. Evans,M.J. (1998) Gene trapping - a preface. Dev. Dyn., 12, 167-169.
9. Gossler,A., Joyner,A.L., Rossant,J. and Skarnes,W.C. (1989) Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science, 244, 463-465.
10. von Melchner,H. and Ruley,H.E. (1989) Identification of cellular promoters by using a retrovirus promoter trap. J. Virol., 63, 3227-3233.
11. Niwa,H., Araki,K., Kimura,S., Taniguchi,S., Wakasugi,S. and Yamamura,K. (1993) An efficient gene-trap method using poly A trap vectors and characterization of gene-trap events. J. Biochem. (Tokyo), 113, 343-349.
12. Salminen,M., Meyer,B.I. and Gruss,P. (1998) Efficient poly A trap approach allows the capture of genes specifically active in differentiated embryonic stem cells and in mouse embryos. Dev. Dyn., 212, 326-333.
13. Ishida,Y. and Leder,P. (1999) RET: a poly A-trap retrovirus vector for reversible disruption and expression monitoring of genes in living cells. Nucleic Acids Res., 27, e35.
14. Xu,R.H., Chen,X., Li,D.S., Li,R., Addicks,G.C., Glennon,C., Zwaka,T.P. and Thomson JA. (2002) BMP4 initiates human embryonic stem cell differentiation to trophoblast. Nat. Biotechnol., 20, 1261-64.
15. Berger,S.L. and Chirgwin,J.M. (1989) Isolation of RNA. Methods Enzymol., 180, 3-13.
16. Kent,W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664.
17. Benjamin,D., Bakel,I.V. and Craig I.W. (2000) A novel expression based approach for assessing the inactivation status of human X-linked genes. Eur. J. Hum. Genet., 8, 103-108.
18. Harlow,E. and Lane,D. (1999) Using Antibodies: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
19. Goodwin,N.C., Ishida,Y., Hartford,S., Wnek,C., Bergstrom,R.A., Leder,P. and Schimenti,J.C. (2001) DelBank: a mouse ES-cell resource for generating deletions. Nature Genet., 28, 310-311.
20. Frohman,M.A., Dush,M.K. and Martin,G.R. (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc. Natl Acad. Sci. USA, 85, 8998-9002.
21. Dvash,T., Mayshar,Y., Darr,H., McElhaney,M., Barker,D., Yanuka,O., Kotkow,K.J., Rubin,L.L., Benvenisty,N. and Eiges,R. (2004) Temporal gene expression during differentiation of human embryonic stem cells and embryoid bodies. Hum. Reprod., in press.
22. Kremer,E.J., Pritchard,M., Lynch,M., Yu,S., Holman,K., Baker,E., Warren,S.T., Schlessinger,D., Sutherland,G.R. and Richards,R.I. (1991) Mapping of DNA instability at the fragile X to a trinucleotide repeat sequence p(CCG)n. Science, 252,1711-1714.
23. Plath,K., Mlynarczyk-Evans,S., Nusinow,D.A. and Panning,B. (2002) Xist RNA and the mechanism of X chromosome inactivation. Annu. Rev. Genet., 36, 233-278.
24. Takagi,N. and Sasaki,M. (1975) Preferential inactivation of the paternally derived X chromosome in the extraembryonic membranes of the mouse. Nature, 256, 640-642.
25. Ropers,B.J.,Wolff,G. and Hitzeroth,H.W. (1978) Preferential X inactivation in human placenta membranes:is the paternal X inactive in early embryonic development of female mammals? Hum. Genet., 43,265-272.
26. Migeon,B.R. and Do,T.T. (1979) In search of non-random X inactivation: studies of fetal membranes heterozygous for glucose-6-phosphate dehydrogenase. Am. J. Hum. Genet., 31, 581-585.
27. Zeng,S.M. and Yankowitz,J. (2003) X-inactivation patterns in human embryonic and extra-embryonic tissues. Placenta, 24, 270-275.
28. Heard,E., Mongelard,F., Arnaud,D., Chureau,C., Vourc'h,C. and Avner,P. (1999) Human XIST yeast artificial chromosome transgenes show partial X inactivation center function in mouse embryonic stem cells. Proc. Natl Acad. Sci. USA, 96, 6841-6846.
29. Migeon,B.R., Winter,H., Kazi,E., Chowdhury,A.K., Hughes,A., Haisley-Royster,C., Morrison,H. and Jeppesen,P. (2001) Low-copy-number human transgene is recognized as an X inactivation center in mouse ES cells, but fails to induce cis-inactivation in chimeric mice. Genomics, 71, 156-162.
30. Disteche,C.M. (1995) Escape from X inactivation in human and mouse. Trends Genet., 11, 17-22.
31. Vasques,L.R., Klockner,M.N. and Pereira,L.V. (2002) X chromosome inactivation: how human are mice? Cytogenet. Genome Res., 99, 30-35.
32. Mortensen,R.M., Conner,D.A., Chao,S., Geisterfer-Lowrance,A.A. and Seidman,J.G. (1992) Production of homozygous mutant ES cells with a single targeting construct. Mol. Cell. Biol., 12, 2391-2395.