ChIP on Chip: Surprising results are often artifacts

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Waldminghaus, Torsten ^a   Skarstad, Kirsten ^a  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN SEQA; RIBONUCLEASE; SIGMA FACTOR; SIGMA FACTOR 32; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; HEAT SHOCK PROTEIN; HEAT SHOCK SIGMA FACTOR 32; HEAT-SHOCK SIGMA FACTOR 32; OUTER MEMBRANE PROTEIN; SEQA PROTEIN, E COLI;

ARTICLE; ARTIFACT; BACTERIAL CHROMOSOME; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA CROSS LINKING; ESCHERICHIA COLI; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; SEQUENCE ANALYSIS; SIGNAL DETECTION; BACTERIAL GENOME; GENETICS; LABORATORY DIAGNOSIS; METABOLISM; METHODOLOGY; PROTEIN MICROARRAY;

ESCHERICHIA;

ARTIFACTS; BACTERIAL OUTER MEMBRANE PROTEINS; BASE SEQUENCE; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOMES, BACTERIAL; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FALSE POSITIVE REACTIONS; GENOME, BACTERIAL; HEAT-SHOCK PROTEINS; PROTEIN ARRAY ANALYSIS; RIBONUCLEASES; SIGMA FACTOR;

EID: 77954169130     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-414     Document Type: Article

References (38)

1. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, et al. Genome-wide location and function of DNA binding proteins. Science 2000, 290(5500):2306-2309.
2. Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004, 83(3):349-360. 10.1016/j.ygeno.2003.11.004, 14986705.
3. Grainger DC, Overton TW, Reppas N, Wade JT, Tamai E, Hobman JL, Constantinidou C, Struhl K, Church G, Busby SJ. Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J Bacteriol 2004, 186(20):6938-6943. 10.1128/JB.186.20.6938-6943.2004, 522211, 15466047.
4. Lee TI, Johnstone SE, Young RA. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 2006, 1(2):729-748. 10.1038/nprot.2006.98, 17406303.
5. Sandmann T, Jakobsen JS, Furlong EE. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nat Protoc 2006, 1(6):2839-2855. 10.1038/nprot.2006.383, 17406543.
6. Waldminghaus T, Skarstad K. The Escherichia coli SeqA protein. Plasmid 2009, 61(3):141-150. 10.1016/j.plasmid.2009.02.004, 19254745.
7. Slater S, Wold S, Lu M, Boye E, Skarstad K, Kleckner N. E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell 1995, 82(6):927-936. 10.1016/0092-8674(95)90272-4, 7553853.
8. Campbell JL, Kleckner N. E. coli oriC and the dnaA gene promoter are sequestered from dam methyltransferase following the passage of the chromosomal replication fork. Cell 1990, 62(5):967-979. 10.1016/0092-8674(90)90271-F, 1697508.
9. Nagy PL, Cleary ML, Brown PO, Lieb JD. Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. P Natl Acad Sci USA 2003, 100(11):6364-6369. 10.1073/pnas.1131966100, 164452, 12750471.
10. Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E. Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Biol 2006, 13(9):806-814. 10.1038/nsmb1130, 16892065.
11. Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA. Regulon and promoter analysis of the E. coli heat-shock factor, σ32, reveals a multifaceted cellular response to heat stress. Genes Dev 2006, 20(13):1776-1789. 10.1101/gad.1428206, 1522074, 16818608.
12. Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res 2008, 18(3):393-403. 10.1101/gr.7080508, 2259103, 18258921.
13. Vora T, Hottes AK, Tavazoie S. Protein occupancy landscape of a bacterial genome. Mol Cell 2009, 35(2):247-253. 10.1016/j.molcel.2009.06.035, 19647521.
14. Bucca G, Laing E, Mersinias V, Allenby N, Hurd D, Holdstock J, Brenner V, Harrison M, Smith CP. Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon. Genome Biol 2009, 10(1):R5. 10.1186/gb-2009-10-1-r5, 2687793, 19146703.
15. Gruber S, Errington J. Recruitment of condensin to replication origin regions by ParB/SpoOJ promotes chromosome segregation in B. subtilis. Cell 2009, 137(4):685-696. 10.1016/j.cell.2009.02.035, 19450516.
16. D'Ambrosio C, Schmidt CK, Katou Y, Kelly G, Itoh T, Shirahige K, Uhlmann F. Identification of cis-acting sites for condensin loading onto budding yeast chromosomes. Genes Dev 2008, 22(16):2215-2227. 10.1101/gad.1675708, 2518811, 18708580.
17. Schmidt CK, Brookes N, Uhlmann F. Conserved features of cohesin binding along fission yeast chromosomes. Genome Biol 2009, 10(5):R52. 10.1186/gb-2009-10-5-r52, 2718518, 19454013.
18. Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ. Normalization and experimental design for ChIP-chip data. BMC Bioinformatics 2007, 8:219. 10.1186/1471-2105-8-219, 1913544, 17592629.
19. Zhao K, Liu M, Burgess RR. The global transcriptional response of Escherichia coli to induced σ32 protein involves σ32 regulon activation followed by inactivation and degradation of σ32 in vivo. J Biol Chem 2005, 280(18):17758-17768. 10.1074/jbc.M500393200, 15757896.
20. Grainger DC, Hurd D, Goldberg MD, Busby SJ. Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res 2006, 34(16):4642-4652. 10.1093/nar/gkl542, 1636352, 16963779.
21. Cho BK, Knight EM, Barrett CL, Palsson BO. Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res 2008, 18(6):900-910. 10.1101/gr.070276.107, 2413157, 18340041.
22. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, et al. Genome-wide analysis of estrogen receptor binding sites. Nat Gen 2006, 38(11):1289-1297. 10.1038/ng1901, 17013392.
23. Gevry N, Hardy S, Jacques PE, Laflamme L, Svotelis A, Robert F, Gaudreau L. Histone H2A.Z is essential for estrogen receptor signaling. Genes Dev 2009, 23(13):1522-1533. 10.1101/gad.1787109, 2704467, 19515975.
24. Andrau JC, van de Pasch L, Lijnzaad P, Bijma T, Koerkamp MG, van de Peppel J, Werner M, Holstege FC. Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA. Mol Cell 2006, 22(2):179-192. 10.1016/j.molcel.2006.03.023, 16630888.
25. Fan X, Chou DM, Struhl K. Activator-specific recruitment of Mediator in vivo. Nat Struct Mol Biol 2006, 13(2):117-120. 10.1038/nsmb1049, 16429153.
26. Zhu X, Wiren M, Sinha I, Rasmussen NN, Linder T, Holmberg S, Ekwall K, Gustafsson CM. Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions. Mol Cell 2006, 22(2):169-178. 10.1016/j.molcel.2006.03.032, 16630887.
27. Fan X, Struhl K. Where does mediator bind in vivo?. PLoS ONE 2009, 4(4):e5029. 10.1371/journal.pone.0005029, 2661142, 19343176.
28. Gordan R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 2009, 19(11):2090-100. 10.1101/gr.094144.109, 2775597, 19652015.
29. Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S. NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility. Mol Microbiol 2009, 73(4):680-94. 10.1111/j.1365-2958.2009.06799.x, 19656291.
30. Efromovich S, Grainger D, Bodenmiller D, Spiro S. Genome-wide identification of binding sites for the nitric oxide-sensitive transcriptional regulator NsrR. Methods Enzymol 2008, 437:211-233. full_text, 18433631.
31. Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrancois P, Struhl K, Gerstein M, Snyder M. Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci USA 2009, 106(35):14926-14931. 10.1073/pnas.0905443106, 2736440, 19706456.
32. Lefrancois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M. Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics 2009, 10:37. 10.1186/1471-2164-10-37, 2656530, 19159457.
33. Lu M, Campbell JL, Boye E, Kleckner N. SeqA: a negative modulator of replication initiation in E. coli. Cell 1994, 77(3):413-426. 10.1016/0092-8674(94)90156-2, 8011018.
34. Brendler T, Sawitzke J, Sergueev K, Austin S. A case for sliding SeqA tracts at anchored replication forks during Escherichia coli chromosome replication and segregation. EMBO J 2000, 19(22):6249-6258. 10.1093/emboj/19.22.6249, 305820, 11080170.
35. Yamazoe M, Adachi S, Kanaya S, Ohsumi K, Hiraga S. Sequential binding of SeqA protein to nascent DNA segments at replication forks in synchronized cultures of Escherichia coli. Mol Microbiol 2005, 55(1):289-298. 10.1111/j.1365-2958.2004.04389.x, 15612935.
36. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
37. Smyth GK, Speed T. Normalization of cDNA microarray data. Methods 2003, 31(4):265-273.
38. Ghai R, Hain T, Chakraborty T. GenomeViz: visualizing microbial genomes. BMC Bioinformatics 2004, 5:198. 10.1186/1471-2105-5-198, 544189, 15601465.