Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray

Methods in Molecular Biology

Volumn 439, Issue , 2008, Pages 131-145

  Cho, Byung Kwan ^a   Knight, Eric M ^a   Palsson, Bernhard Ø ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

ChIP chip; Chromatin immunoprecipitation; Microarray; RNA polymerase; Transcription factor; Transcription factor binding

Indexed keywords

ESCHERICHIA COLI;

EID: 84934439157     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-188-8_9     Document Type: Article

References (28)

1. Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, WuY, Green RD, Ren B (2005) A high-resolution map of active promoters in the human genome. Nature 436:876-880
2. Ren B, Robert R, Wyrick JJ, Aparicio O, Jennings EG, Simon I. Zeitlinger J, Schreiber J, Hannett,N, Kanin E, Volke« TL,Wilson CJ, Bell SP, Young RA (2000) Genome-wide resolution and function of DNA binding proteins. Science 290:2306-2309
3. Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BO (2005) Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarray. J Bacteriol 187:6166-6174
4. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne J, Volkert TL, Fraenkel E, Gifford DK, Young RA (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804
5. Wardle FC, Odom DT, Bell GW, Yuan B, Danford TW, Wiellette EL, Herbolsheimer E, Sive HL, Young RA, Smith JC (2006) Zebrafish promoter microarrays identify actively transcribed embryonic genes. Genome Biol 7:R71
6. Gilchrist M, Thorsson V, Li B, Rust AG, Korb M, Kennedy K, Hai T, Bolouri H, Aderem A (2006) Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441:173-178
7. Orian A, Steensel BV, Delrow J, Bussemaker HJ, Li L, Sawado T, Williams E, Loo LWM, Cowley SM, Yost C, Pierce S, Edgar BA, Parkhurst,SM, Eisenman RN (2003) Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev. 17, 1101-1114.
8. Chua YL, Mott E, Brown AP, MacLean D, Gray JC (2004) Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones. Plant J 37:789-800
9. Grainger DC, Hurd D, Harrison M, Holdstock J, Busby JW (2005) Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc Natl Acad Sci USA 102:17693-17698
10. Carter NP, Vetrie D (2004) Applications of genomic microarrays to explore human chromosome structure and function. Hum Mol Genet 13:R297-R302
11. MacAlpine DM, Bell SP (2005) A genomic view of eukaryotic DNA replication. Chromosome Res 13:309-326
12. Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T (2006) A systems approach to mapping DNA damage response pathways. Science 312:1054-1059
13. Wade JT, Roa DC, Grainger DC, Hurd D, Busby JW, Struhl K, Nudler E (2006) Extensive functional overlap between a factors in Escherichia coli. Nat Struct Mol Biol, doi: 10.1038/nsmb1130
14. Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M (2004) Regulation of gene expression by a metabolic enzyme. Science 306:482-484
15. Kim TH, Ren B (2006) Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet 7:81-102
16. Lee TI, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protocols 1:729-748
17. Buck MJ, Lieb JD (2004) ChIP-chip: Consideration for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83:349-360
18. Negre N, Lavrov S, Hennetin J, Bellis M, Cavalli G (2006) Mapping the distribution of chromatin proteins by ChIP on Chip. Methods Enzymol 410:316-341
19. Hecht A, Grunstein M (1999) Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. Methods Enzymol 304:399-414
20. Ren B,d Dynlacht BD (2004) Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol 376:304-315
21. Cho BK, Knight EM, Palsson BØ (2006) PCR-based tandem epitope tagging system for Escherichia coli genome engineering. Biotechniques 40:67-72
22. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538
23. Buck MJ, Nobel AB, Lieb JD (2005) ChIPOTIe: A user-friendly tool for the analysis of ChIPchip data. Genome Biol 6:R97
24. Bieda M, Xu X, Singer MA, Green R, Farnham PJ (2006) Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res 16:595-605
25. Ji H, Wong WH (2005) TileMap: Create chromosomal map of tiling array hybridizations. Bioinformatics 21:3629-3636
26. Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK (2006) High-resolution computational models of genome binding events. Nat Biotechnol 24:963-970
27. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS (2006) Modelbased analysis of tiling-arrays for ChlP-chip. Proc Natl Acad Sci USA 103:12457-12462
28. Gibbons FD, Proft M, Struhl K, Roth FP (2005) Chipper: Discovering transcription-factor targets from chromatin immunoprecipitation microarray using variance stabilization. Genome Biol 6:R96