Mapping the Distribution of Chromatin Proteins by ChIP on Chip

Methods in Enzymology

Volumn 410, Issue , 2006, Pages 316-341

  Nègre, Nicolas ^a   Lavrov, Sergey ^a   Hennetin, Jérôme ^a   Bellis, Michel ^a   Cavalli, Giacomo ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

BIOINFORMATICS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DATA ANALYSIS; DNA DETERMINATION; DNA HYBRIDIZATION; DNA SEQUENCE; DROSOPHILA; GENE MAPPING; NONHUMAN; PRIORITY JOURNAL; QUALITY CONTROL; REVIEW;

CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOMAL PROTEINS, NON-HISTONE; HISTONES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 33747835616     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(06)10015-4     Document Type: Review

References (21)

1. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C., Rogers Y.H., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Gabor G.L., Abril J.F., Agbayani A., An H.J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., and Venter J.C. The genome sequence of Drosophila melanogaster. Science 287 5461 (2000) 2185-2195
2. Arbeitman M.N., Furlong E.E., Imam F., Johnson E., Null B.H., Baker B.S., Krasnow M.A., Scott M.P., Davis R.W., and White K.P. Gene expression during the life cycle of Drosophila melanogaster. Science 297 5590 (2002) 2270-2275
3. Bloyer S., Cavalli G., Brock H.W., and Dura J.M. Identification and characterization of polyhomeotic PREs and TREs. Dev. Biol. 261 2 (2003) 426-442
4. de Boer E., Rodriguez P., Bonte E., Krijgsveld J., Katsantoni E., Heck A., Grosveld F., and Strouboulis J. Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc. Natl. Acad. Sci. USA 100 13 (2003) 7480-7485
5. Francis N.J., Saurin A.J., Shao Z., and Kingston R.E. Reconstitution of a functional core polycomb repressive complex. Mol. Cell 8 3 (2001) 545-556
6. Franke A., DeCamillis M., Zink D., Cheng N., Brock H.W., and Paro R. Polycomb and polyhomeotic are constituents of a multimeric protein complex in chromatin of Drosophila melanogaster. EMBO J. 11 8 (1992) 2941-2950
7. Gupta V., and Oliver B. Drosophila microarray platforms. Brief Funct. Genom. Proteom. 2 2 (2003) 97-105
8. Hennetin J., and Bellis M. Clustering methods for analyzing large data sets: Gonad development, a study case. Methods Enzymol. 411 (2006) 387-407
9. Kirmizis A., Bartley S.M., Kuzmichev A., Margueron R., Reinberg D., Green R., and Farnham P.J. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev. 18 13 (2004) 1592-1605
10. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Carter N., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., Frazier M., Gibbs R.A., Muzny D.M., Scherer S.E., Bouck J.B., Sodergren E.J., Worley K.C., Rives C.M., Gorrell J.H., Metzker M.L., Naylor S.L., Kucherlapati R.S., Nelson D.L., Weinstock G.M., Sakaki Y., Fujiyama A., Hattori M., Yada T., Toyoda A., Itoh T., Kawagoe C., Watanabe H., Totoki Y., Taylor T., Weissenbach J., Heilig R., Saurin W., Artiguenave F., Brottier P., Bruls T., Pelletier E., Robert C., Wincker P., Smith D.R., Doucette-Stamm L., Rubenfield M., Weinstock K., Lee H.M., Dubois J., Rosenthal A., Platzer M., Nyakatura G., Taudien S., Rump A., Yang H., Yu J., Wang J., Huang G., Gu J., Hood L., Rowen L., Madan A., Qin S., Davis R.W., Federspiel N.A., Abola A.P., Proctor M.J., Myers R.M., Schmutz J., Dickson M., Grimwood J., Cox D.R., Olson M.V., Kaul R., Raymond C., Shimizu N., Kawasaki K., Minoshima S., Evans G.A., Athanasiou M., Schultz R., Roe B.A., Chen F., Pan H., Ramser J., Lehrach H., Reinhardt R., McCombie W.R., de la Bastide M., Dedhia N., Blocker H., Hornischer K., Nordsiek G., Agarwala R., Aravind L., Bailey J.A., Bateman A., Batzoglou S., Birney E., Bork P., Brown D.G., Burge C.B., Cerutti L., Chen H.C., Church D., Clamp M., Copley R.R., Doerks T., Eddy S.R., Eichler E.E., Furey T.S., Galagan J., Gilbert J.G., Harmon C., Hayashizaki Y., Haussler D., Hermjakob H., Hokamp K., Jang W., Johnson L.S., Jones T.A., Kasif S., Kaspryzk A., Kennedy S., Kent W.J., Kitts P., Koonin E.V., Korf I., Kulp D., Lancet D., Lowe T.M., McLysaght A., Mikkelsen T., Moran J.V., Mulder N., Pollara V.J., Ponting C.P., Schuler G., Schultz J., Slater G., Smit A.F., Stupka E., Szustakowski J., Thierry-Mieg D., Thierry-Mieg J., Wagner L., Wallis J., Wheeler R., Williams A., Wolf Y.I., Wolfe K.H., Yang S.P., Yeh R.F., Collins F., Guyer M.S., Peterson J., Felsenfeld A., Wetterstrand K.A., Patrinos A., Morgan M.J., de Jong P., Catanese J.J., Osoegawa K., Shizuya H., Choi S., and Chen Y.J. Initial sequencing and analysis of the human genome. Nature 409 6822 (2001) 860-921
11. Liu Z.R., Sargueil B., and Smith C.W. Methylene blue-mediated cross-linking of proteins to double-stranded RNA. Methods Enzymol. 318 (2000) 22-33
12. Martin D.E., Demougin P., Hall M.N., and Bellis M. Rank difference analysis of microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data. BMC Bioinformat. 5 1 (2004) 148
13. Min J., Zhang Y., and Xu R.M. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17 15 (2003) 1823-1828
14. Negre N., Hennetin J., Sun L.V., Lavrov S., Bellis M., White K.P., and Cavalli G. Chromosomal distribution of PcG proteins during Drosophila development. PLOS Biol. 4 (2006) e170
15. Orlando V., Strutt H., and Paro R. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11 2 (1997) 205-214
16. Ren B., Robert F., Wyrick J.J., Aparicio O., Jennings E.G., Simon I., Zeitlinger J., Schreiber J., Hannett N., Kanin E., Volkert T.L., Wilson C.J., Bell S.P., and Young R.A. Genome-wide location and function of DNA binding proteins. Science 290 5500 (2000) 2306-2309
17. Ringrose L., and Paro R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38 (2004) 413-443
18. Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 5235 (1995) 467-470
19. Simon J., Chiang A., Bender W., Shimell M.J., and O'Connor M. Elements of the Drosophila bithorax complex that mediate repression by Polycomb group products. Dev. Biol. 158 1 (1993) 131-144
20. Stolc V., Gauhar Z., Mason C., Halasz G., van Batenburg M.F., Rifkin S.A., Hua S., Herreman T., Tongprasit W., Barbano P.E., Bussemaker H.J., and White K.P. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306 5696 (2004) 655-660
21. Zhang L., Zhang K., Prandl R., and Schoffl F. Detecting DNA-binding of proteins in vivo by UV-crosslinking and immunoprecipitation. Biochem. Biophys. Res. Commun. 322 3 (2004) 705-711