Nanobody-based chromatin immunoprecipitation

Methods in Molecular Biology

Volumn 911, Issue , 2012, Pages 491-505

  Duc, Trong Nguyen ^a,b   Hassanzadeh Ghassabeh, Gholamreza ^a,b   Saerens, Dirk ^a,c   Peeters, Eveline ^c   Charlier, Daniel ^c   Muyldermans, Serge ^a,c  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b Laboratory of Cellular and Molecular Immunology   (Belgium)

^c VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

Author keywords

Chromatin immunoprecipitation; DNA protein interaction; Nanobody; Single domain antibody; Sulfolobus solfataricus

Indexed keywords

NANOBODY; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR LRPB; TRANSCRIPTION FACTOR SS; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; GENOME ANALYSIS; NONHUMAN; PRIORITY JOURNAL; SULFOLOBUS SOLFATARICUS; THERMOACIDOPHILE;

EID: 84934440830     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-968-6_31     Document Type: Article

References (16)

1. Grogan DW (2000) The question of DNA repair in hyperthermophilic archaea. Trends Microbiol 8:180-185
2. She Q et al (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci USA 98:7835-7840
3. Orlando V (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked chro-matin immunoprecipitation. Trends Biochem Sci 25:99-104
4. Orlando V, Strutt H, Paro R (1997) Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11:205-214
5. Nelson JD, Denisenko O, Bomsztyk K (2006) Protocol for the fast chromatin immunopre-cipitation (ChIP) method. Nat Protoc 1:179-185
6. Haring M et al (2007) Chromatin immuno-precipitation: optimization, quantitative analysis and data normalization. Plant Methods 3:11
7. Weinmann AS, Farnham PJ (2002) Identi fication of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 26:37-47
8. Dahl JA, Collas P (2007) Q2ChIP, a quick and quantitative chromatin immunoprecipitation assay, unravels epigenetic dynamics of develop-mentally regulated genes in human carcinoma cells. Stem Cells 25:1037-1046
9. Mukhopadhyay A et al (2008) Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat Protoc 3:698-709
10. Wells J, Farnham PJ (2002) Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 26:48-56
11. Carroll JS et al (2006) Genome-wide analysis of estrogen receptor binding sites. Nat Genet 38:1289-1297
12. Impey S et al (2004) De fining the CREB regu-lon: a genome-wide analysis of transcription factor regulatory regions. Cell 119: 1041-1054
13. Robertson G et al (2007) Genome-wide pro files of STAT1 DNA association using chro-matin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651-657
14. Peeters E et al (2004) Ss-LrpB, a novel Lrp-like regulator of Sulfolobus solfataricus P2, binds cooperatively to three conserved targets in its own control region. Mol Microbiol 54: 321-336
15. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-[Delta][Delta]CT method. Methods 25:402-408
16. Fan X et al (2008) Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immuno-precipitation experiments. Nucl Acids Res 36:e125