3,263
Views
14
CrossRef citations to date
0
Altmetric
Methods and Technical Advances

Bi-functional cross-linking reagents efficiently capture protein-DNA complexes in Drosophila embryos

, , , , &
Pages 43-51 | Received 01 Oct 2013, Accepted 14 Oct 2013, Published online: 13 Dec 2013

References

  • Ghavi-Helm Y, Furlong EE. Analyzing transcription factor occupancy during embryo development using ChIP-seq. Methods Mol Biol 2012; 786:229 - 45; http://dx.doi.org/10.1007/978-1-61779-292-2_14; PMID: 21938630
  • Li XY, Biggin MD. Genome-wide in vivo cross-linking of sequence-specific transcription factors. Methods Mol Biol 2012; 809:3 - 26; http://dx.doi.org/10.1007/978-1-61779-376-9_1; PMID: 22113265
  • Gilmour DS, Lis JT. Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes. Proc Natl Acad Sci U S A 1984; 81:4275 - 9; http://dx.doi.org/10.1073/pnas.81.14.4275; PMID: 6379641
  • Gilmour DS, Lis JT. In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster. Mol Cell Biol 1985; 5:2009 - 18; PMID: 3018544
  • Gilmour DS, Rougvie AE, Lis JT. Protein-DNA cross-linking as a means to determine the distribution of proteins on DNA in vivo. Methods Cell Biol 1991; 35:369 - 81; http://dx.doi.org/10.1016/S0091-679X(08)60580-4; PMID: 1664030
  • Solomon MJ, Larsen PL, Varshavsky A. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 1988; 53:937 - 47; http://dx.doi.org/10.1016/S0092-8674(88)90469-2; PMID: 2454748
  • Dedon PC, Soults JA, Allis CD, Gorovsky MA. A simplified formaldehyde fixation and immunoprecipitation technique for studying protein-DNA interactions. Anal Biochem 1991; 197:83 - 90; http://dx.doi.org/10.1016/0003-2697(91)90359-2; PMID: 1952079
  • Orlando V, Paro R. Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell 1993; 75:1187 - 98; http://dx.doi.org/10.1016/0092-8674(93)90328-N; PMID: 7903220
  • Aoki T, Sarkeshik A, Yates J, Schedl P. Elba, a novel developmentally regulated chromatin boundary factor is a hetero-tripartite DNA binding complex. Elife 2012; 1:e00171; http://dx.doi.org/10.7554/eLife.00171; PMID: 23240086
  • Aoki T, Schweinsberg S, Manasson J, Schedl P. A stage-specific factor confers Fab-7 boundary activity during early embryogenesis in Drosophila. Mol Cell Biol 2008; 28:1047 - 60; http://dx.doi.org/10.1128/MCB.01622-07; PMID: 18039839
  • Mihaly J, Hogga I, Gausz J, Gyurkovics H, Karch F. In situ dissection of the Fab-7 region of the bithorax complex into a chromatin domain boundary and a Polycomb-response element. Development 1997; 124:1809 - 20; PMID: 9165128
  • Nowak DE, Tian B, Brasier AR. Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation. Biotechniques 2005; 39:715 - 25; http://dx.doi.org/10.2144/000112014; PMID: 16315372
  • Dai Q, Ren A, Westholm JO, Serganov AA, Patel DJ, Lai EC. The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors. Genes Dev 2013; 27:602 - 14; http://dx.doi.org/10.1101/gad.213314.113; PMID: 23468431
  • Kurdistani SK, Grunstein M. In vivo protein-protein and protein-DNA crosslinking for genomewide binding microarray. Methods 2003; 31:90 - 5; http://dx.doi.org/10.1016/S1046-2023(03)00092-6; PMID: 12893178
  • Zeng PY, Vakoc CR, Chen ZC, Blobel GA, Berger SL. In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation. Biotechniques 2006; 41:694 - , 696, 698; http://dx.doi.org/10.2144/000112297; PMID: 17191611
  • Fujita N, Wade PA. Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes. Methods 2004; 33:81 - 5; http://dx.doi.org/10.1016/j.ymeth.2003.10.022; PMID: 15039090
  • Kappes G, Deshpande G, Mulvey BB, Horabin JI, Schedl P. The Drosophila Myc gene, diminutive, is a positive regulator of the Sex-lethal establishment promoter, Sxl-Pe. Proc Natl Acad Sci U S A 2011; 108:1543 - 8; http://dx.doi.org/10.1073/pnas.1017006108; PMID: 21220321
  • Barges S, Mihaly J, Galloni M, Hagstrom K, Müller M, Shanower G, Schedl P, Gyurkovics H, Karch F. The Fab-8 boundary defines the distal limit of the bithorax complex iab-7 domain and insulates iab-7 from initiation elements and a PRE in the adjacent iab-8 domain. Development 2000; 127:779 - 90; PMID: 10648236
  • Holohan EE, Kwong C, Adryan B, Bartkuhn M, Herold M, Renkawitz R, Russell S, White R. CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex. PLoS Genet 2007; 3:e112; http://dx.doi.org/10.1371/journal.pgen.0030112; PMID: 17616980
  • Ciavatta D, Rogers S, Magnuson T. Drosophila CTCF is required for Fab-8 enhancer blocking activity in S2 cells. J Mol Biol 2007; 373:233 - 9; http://dx.doi.org/10.1016/j.jmb.2007.07.065; PMID: 17825318
  • Cavalli G, Orlando V, Paro R. Mapping DNA target sites of chromatin associated proteins by formaldehyde cross-linking in Drosophila embryos. In: Bickmore WA, ed. Chromosome Structural Analysis: A Practical Approach. New York: Oxford University Press, 1999:20–37.
  • Toth J, Biggin MD. The specificity of protein-DNA crosslinking by formaldehyde: in vitro and in drosophila embryos. Nucleic Acids Res 2000; 28:e4; http://dx.doi.org/10.1093/nar/28.2.e4; PMID: 10606672

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.