The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos

Methods

Volumn 62, Issue 3, 2013, Pages 207-215

  Bogdanović, Ozren ^a   Fernández Miñán, Ana ^a   Tena, Juan J ^a   de la Calle Mustienes, Elisa ^a   Gómez Skarmeta, José Luis ^a  

^a Instituto de Salud Carlos III   (Spain)

Author keywords

Development; DNA methylation; Epigenomics; Histone modifications; Zebrafish

Indexed keywords

GENOMIC DNA; HISTONE;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA METHYLATION; EMBRYO; EMBRYO DEVELOPMENT; EPIGENETICS; FEMALE; GENE EXPRESSION PROFILING; GENE SEQUENCE; HISTONE MODIFICATION; MALE; NONHUMAN; PRIORITY JOURNAL; ZEBRA FISH;

DANIO RERIO; VERTEBRATA;

DEVELOPMENT; DNA METHYLATION; EPIGENOMICS; HISTONE MODIFICATIONS; ZEBRAFISH;

ANIMALS; DNA METHYLATION; EMBRYO, NONMAMMALIAN; EMBRYONIC DEVELOPMENT; EPIGENESIS, GENETIC; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONES; LAB-ON-A-CHIP DEVICES; PROTEIN PROCESSING, POST-TRANSLATIONAL; ZEBRAFISH;

EID: 84883231829     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.04.011     Document Type: Article

References (48)

1. Santos-Rosa H., Schneider R., Bannister A.J., Sherriff J., Bernstein B.E., et al. Nature 2002, 419:407-411.
2. Czermin B., Melfi R., McCabe D., Seitz V., Imhof A., et al. Cell 2002, 111:185-196.
3. Muller J., Hart C.M., Francis N.J., Vargas M.L., Sengupta A., et al. Cell 2002, 111:197-208.
4. Heintzman N.D., Hon G.C., Hawkins R.D., Kheradpour P., Stark A., et al. Nature 2009, 459:108-112.
5. Rada-Iglesias A., Bajpai R., Swigut T., Brugmann S.A., Flynn R.A., et al. Nature 2011, 470:279-283.
6. Creyghton M.P., Cheng A.W., Welstead G.G., Kooistra T., Carey B.W., et al. Proc Natl Acad Sci USA 2010, 107:21931-21936.
7. Robertson G., Hirst M., Bainbridge M., Bilenky M., Zhao Y., et al. Nat. Methods 2007, 4:651-657.
8. Schmidt D., Wilson M.D., Spyrou C., Brown G.D., Hadfield J., et al. Methods 2009, 48:240-248.
9. Ho J.W., Bishop E., Karchenko P.V., Negre N., White K.P., et al. BMC Genomics 2011, 12:134.
10. Weber M., Davies J.J., Wittig D., Oakeley E.J., Haase M., et al. Nat. Genet. 2005, 37:853-862.
11. Lister R., Pelizzola M., Dowen R.H., Hawkins R.D., Hon G., et al. Nature 2009, 462:315-322.
12. Bogdanovic O., Veenstra G.J. BMC Res. Notes 2011, 4:300.
13. Smith Z.D., Gu H., Bock C., Gnirke A., Meissner A. Methods 2009, 48:226-232.
14. Brinkman A.B., Simmer F., Ma K., Kaan A., Zhu J., et al. Methods 2010, 52:232-236.
15. Harris R.A., Wang T., Coarfa C., Nagarajan R.P., Hong C., et al. Nat. Biotechnol. 2010, 28:1097-1105.
16. Bock C., Tomazou E.M., Brinkman A.B., Muller F., Simmer F., et al. Nat. Biotechnol. 2010, 28:1106-1114.
17. Borgel J., Guibert S., Li Y., Chiba H., Schubeler D., et al. Nat. Genet. 2010, 42:1093-1100.
18. Matarese F., Carrillo-de Santa Pau E., Stunnenberg H.G. Mol. Syst. Biol. 2011, 7:562.
19. Meehan R.R., Lewis J.D., Bird A.P. Nucleic Acids Res. 1992, 20:5085-5092.
20. Lewis J.D., Meehan R.R., Henzel W.J., Maurer-Fogy I., Jeppesen P., et al. Cell 1992, 69:905-914.
21. Bogdanovic O., Long S.W., van Heeringen S.J., Brinkman A.B., Gomez-Skarmeta J.L., et al. Genome Res. 2011, 21:1313-1327.
22. Aday A.W., Zhu L.J., Lakshmanan A., Wang J., Lawson N.D. Dev. Biol. 2011, 357:450-462.
23. Akkers R.C., van Heeringen S.J., Jacobi U.G., Janssen-Megens E.M., Francoijs K.J., et al. Dev. Cell 2009, 17:425-434.
24. Bogdanovic O., Fernández-Miñán A., Tena J.J., de la Calle-Mustienes E., Hidalgo C., van Kruysbergen I., van Heeringen S.J., Veenstra G.J., Gómez-Skarmeta J.L. Genome Res. 2012, 22:2043-2053.
25. Lindeman L.C., Andersen I.S., Reiner A.H., Li N., Aanes H., et al. Dev. Cell 2011, 21:993-1004.
26. Vastenhouw N.L., Zhang Y., Woods I.G., Imam F., Regev A., et al. Nature 2010, 464:922-926.
27. Andersen I.S., Reiner A.H., Aanes H., Alestrom P., Collas P. Genome Biol. 2012, 13:R65.
28. Kimmel C.B. Trends Genet. 1989, 5:283-288.
29. Driever W., Solnica-Krezel L., Schier A.F., Neuhauss S.C., Malicki J., et al. Development 1996, 123:37-46.
30. Fishman M.C. Science 2001, 294:1290-1291.
31. Lieschke G.J., Currie P.D. Nat. Rev. Genet. 2007, 8:353-367.
32. Wardle F.C., Odom D.T., Bell G.W., Yuan B., Danford T.W., et al. Genome Biol. 2006, 7:R71.
33. Marrable A.W. J. Embryol. Exp. Morphol. 1965, 14:15-24.
34. Kim D.H., Sun Y., Yun S., Kim B., Hwang C.N., et al. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2004, 7:5061-5064.
35. Zhang Y., Liu T., Meyer C.A., Eeckhoute J., Johnson D.S., et al. Genome Biol. 2008, 9:R137.
36. Rozen S., Skaletsky H. Methods Mol. Biol. 2000, 132:365-386.
37. Brinkman A.B., Roelofsen T., Pennings S.W., Martens J.H., Jenuwein T., et al. EMBORep. 2006, 7:628-634.
38. Pauli A., Valen E., Lin M.F., Garber M., Vastenhouw N.L., et al. Genome Res. 2012, 22:577-591.
39. B. Thisse, S. Pfumio, M. Fürthauer, B. Loppin, V. Heyer, et al., Expression of the zebrafish genome during embryogenesis, ZFIN on-line publication, 2001.
40. Bessa J., Tena J.J., de la Calle-Mustienes E., Fernandez-Minan A., Naranjo S., et al. Dev. Dyn. 2009, 238:2409-2417.
41. Irimia M., Tena J.J., Alexis M.S., Fernandez-Minan A., Maeso I., et al. Genome Res. 2012, 22:2356-2367.
42. Tena J.J., Alonso M.E., de la Calle-Mustienes E., Splinter E., de Laat W., et al. Nat. Commun. 2011, 2:310.
43. de la Calle-Mustienes E., Feijoo C.G., Manzanares M., Tena J.J., Rodriguez-Seguel E., et al. Genome Res. 2005, 15:1061-1072.
44. Bonn S., Zinzen R.P., Perez-Gonzalez A., Riddell A., Gavin A.C., et al. Nat. Protoc. 2012, 7:978-994.
45. Shankaranarayanan P., Mendoza-Parra M.A., Walia M., Wang L., Li N., et al. Nat. Methods 2011, 8:565-567.
46. Yamakoshi K., Shimoda N. Genesis 2003, 37:195-202.
47. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., et al. Genome Res. 2002, 12:996-1006.
48. Margueron R., Reinberg D. Nat. Rev. Genet. 2010, 11:285-296.