ChIP for hox proteins from Drosophila imaginal discs

Methods in Molecular Biology

Volumn 1196, Issue , 2014, Pages 241-253

  Agrawal, Pavan ^a   Shashidhara, L S ^a  

^a NONE

Author keywords

Chromatin immunoprecipitation; Drosophila; GAGA factor; Haltere; Hox; Imaginal discs; Ubx; Wing

Indexed keywords

HOX PROTEIN; PROTEIN A; SEPHAROSE; CHROMATIN; HOMEODOMAIN PROTEIN;

ANIMAL CELL; ANIMAL TISSUE; ANTIGEN BINDING; ARTICLE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA PURIFICATION; DROSOPHILA; IMAGINAL DISC; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CROSS LINKING; PROTEIN DNA INTERACTION; ANIMAL; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; PROCEDURES;

ANIMALS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DROSOPHILA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOMEODOMAIN PROTEINS; IMAGINAL DISCS;

EID: 84927555762     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1242-1_15     Document Type: Article

References (20)

1. Ren B, Robert F, Wyrick JJ et al (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306-2309. doi: 10.1126/science.290.5500.2306
2. Iyer VR, Horak CE, Scafe CS et al (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538. doi: 10.1038/35054095
3. Wu J, Smith LT, Plass C, Huang TH-M (2006) ChIP-chip comes of age for genomewide functional analysis. Cancer Res 66:6899-6902. doi: 10.1158/0008-5472.CAN-06-0276
4. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669-680. doi: 10.1038/nrg2641
5. Agrawal P, Habib F, Yelagandula R, Shashidhara LS (2011) Genome-level identifi cation of targets of Hox protein Ultrabithorax in Drosophila: novel mechanisms for target selection. Sci Rep 1:1-10. doi: 10.1038/srep00205
6. Li X, MacArthur S, Bourgon R et al (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6:e27. doi: 10.1371/journal.pbio.0060027
7. Negre N, Brown CD, Ma L et al (2011) A cis-regulatory map of the Drosophila genome. Nature 471:527-531. doi: 10.1038/nature09990
8. Bonn S, Zinzen RP, Perez-Gonzalez A et al (2012) Cell type-specifi c chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat Protoc 7:978-994. doi: 10.1038/nprot.2012.049
9. Shankaranarayanan P, Walia M, Wang L et al (2011) Single-tube linear DNA amplifi cation (LinDA) for robust ChiP-seq. Nat Methods 8:565-568. doi: 10.1038/nmeth.1626
10. Ng J-H, Kumar V, Muratani M et al (2013) In vivo epigenomic profi ling of germ cells reveals germ cell molecular signatures. Dev Cell 24:324-333. doi: 10.1016/j.devcel.2012.12.011
11. Collas P (2009) Chromatin immunoprecipitation assays. In: Collas P (ed) Methods in molecular biology, 567th edn. Humana, Totowa, NJ, pp 1-25
12. Noyes MB, Christensen RG, Wakabayashi A et al (2008) Analysis of homeodomain specifi cities allows the family-wide prediction of preferred recognition sites. Cell 133:1277-1289, doi: http://dx.doi.org/10.1016/j.cell.2008.05.023
13. Slattery M, Ma L, Négre N et al (2011) Genomewide tissue-specifi c occupancy of the Hox protein Ultrabithorax and Hox cofactor homothorax in Drosophila. PLoS One 6:e14686. doi: 10.1371/journal.pone.0014686
14. Choo SW, White R, Russell S (2011) Genomewide analysis of the binding of the Hox protein Ultrabithorax and the Hox cofactor homothorax in Drosophila. PLoS One 6:e14778. doi: 10.1371/journal.pone.0014778
15. Hersh BM, Carroll SB (2005) Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis-regulatory elements in Drosophila. Development 132:1567-1577. doi: 10.1242/dev.01737
16. Hersh BM, Nelson CE, Stoll SJ et al (2007) The UBX-regulated network in the haltere imaginal disc of D. melanogaster. Dev Biol 302:717-727. doi: 10.1016/j.ydbio.2006.11.011
17. Makhijani K, Kalyani C, Srividya T, Shashidhara LS (2007) Modulation of Decapentaplegic gradient during haltere specifi cation in Drosophila. Dev Biol 302:243-255. doi: 10.1016/j.ydbio.2006.09.029
18. Bustin SA, Benes V, Garson JA et al (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55:611-622. doi: 10.1373/clinchem.2008.112797
19. Manoonkitiwongsa PS, Schultz RL (2003) Proper nomenclature of formaldehyde and paraformaldehyde fi xatives for histochemistry. Histochem J 34:365-367. doi: 10.102 3/A:1023342929105
20. Lee TI, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarraybased analysis of protein location. Nat Protoc 1:729-748. doi: 10.1038/nprot2006.98