ORGANIC
ORGANIC
ORGANIC is a gentle protocol that avoids crosslinking and sonication. The method is a combination of MNase-Seq and native ChIP that provides accurate maps of chromatin-occupied regions in complex eukaryotic genomes.
Pros:
- Avoids sonication bias1
- Avoids crosslinking artifacts2
Cons:
- Potentially poor solubilization of proteins2
- MNase sequence bias 3
- Nuclei isolation may introduce artifacts
- Not replicated in other laboratories
- ORGANIC: Kasinathan S., Orsi G. A., Zentner G. E., Ahmad K. and Henikoff S. (2013) High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods advance online publication:
- 1. Teytelman L., Ozaydin B., Zill O., Lefrancois P., Snyder M., et al. (2009) Impact of chromatin structures on DNA processing for genomic analyses. PLoS One 4: e6700
- 2. Zentner G. E. and Henikoff S. (2014) High-resolution digital profiling of the epigenome. Nat Rev Genet 15: 814-827
- 3. Kensche P. R., Hoeijmakers W. A., Toenhake C. G., Bras M., Chappell L., et al. (2016) The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences. Nucleic Acids Res 44: 2110-2124
- Kasinathan S., Orsi G. A., Zentner G. E., Ahmad K. and Henikoff S. (2013) High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods advance online publication:
- Zentner G. E. and Henikoff S. (2014) High-resolution digital profiling of the epigenome. Nat Rev Genet 15: 814-827