ChIP-Exo: An exonuclease based improvement to the accuracy of CHIP-Seq technique

On: Rhee and Pugh, 2011 in Cell.

When DNA microarray techniques were combined with Chromatin Immunoprecipitation (ChIP) method, the protein-DNA interaction analyses promoted to the genome-wide level: ChIP-on-chip. Although microarrays have intrinsic shortcomings such as nonspecific noise and limited genome covering, ChIP-on-chip was the state-of-the art technique (for DNA-protein interaction research) at the beginnings of the 2000s. In the second half of the decade, genome-wide analyses have jumped up several steps with next generation sequencing technology: ChIP-seq. In the latest issue of Cell, Rhee and Pugh further improved the accuracy of ChIP-seq.

ChIP-Exo uses 5'-3' (lambda) exonuclease to chop up 5' ends of the immunoprecipitated DNA protein complexes. The exonuclease stops however, because of the DNA binding protein hindrance. Since the enzyme does not cut 3' ends, the protruding ends are still available to map the DNA to the genome but the technique adds accuracy by gaining the almost exact location of the protein on DNA. The theoretical drawback is the presence of other crosslinked proteins on DNA. In this direction, the authors confirmed that the presence of nucleosomes does not prevent nuclease activity. The de novo motif search revealed recognition sites of a number of transcription factors very accurately.

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
Rhee, HoSung; Pugh, B.Franklin
Cell doi:10.1016/j.cell.2011.11.013 (volume 147 issue 6 pp.1408 - 1419)