Efficient double fragmentation ChiP-seq provides nucleotide resolution protein-DNA binding profiles

39Citations
Citations of this article
120Readers
Mendeley users who have this article in their library.

Abstract

Immunoprecipitated crosslinked protein-DNA fragments typically range in size from several hundred to several thousand base pairs, with a significant part of chromatin being much longer than the optimal length for next-generation sequencing (NGS) procedures. Because these larger fragments may be non-random and represent relevant biology that may otherwise be missed, but also because they represent a significant fraction of the immunoprecipitated material, we designed a double-fragmentation ChIP-seq procedure. After conventional crosslinking and immunoprecipitation, chromatin is decrosslinked and sheared a second time to concentrate fragments in the optimal size range for NGS. Besides the benefits of increased chromatin yields, the procedure also eliminates a laborious size-selection step. We show that the doublefragmentation ChIP-seq approach allows for the generation of biologically relevant genome-wide protein-DNA binding profiles from sub-nanogram amounts of TCF7L2/TCF4, TBP and H3K4me3 immunoprecipitated material. Although optimized for the AB/SOLiD platform, the same approach may be applied to other platforms. © 2010 Mokry et al.

Cite

CITATION STYLE

APA

Mokry, M., Hatzis, P., de Bruijn, E., Koster, J., Versteeg, R., Schuijers, J., … Cuppen, E. (2010). Efficient double fragmentation ChiP-seq provides nucleotide resolution protein-DNA binding profiles. PLoS ONE, 5(11). https://doi.org/10.1371/journal.pone.0015092

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free