What are the disadvantages of Cross-linking ChIP?

One drawback is that precipitation is generally very inefficient, and results in a small yield. Because of this, PCR precipitated DNA is usually required. Another disadvantage is that chemical fixation is required for the samples. Additionally, for some applications, the cross-linked protein-DNA complex must be purified by isopycnic centrifugation through cesium chloride, which is a long and costly procedure. Another limitation is that this technique cannot capture chromatin from cells in their native state, like native ChIP can. Cross-linked chromatin can also mask epitopes of some antibodies, affecting chromatin/antibody binding. Lastly, there is a risk that the cross-linking step may fix interactions which are temporary and hold minor functional significance. Another disadvantage of X-ChIP is that excess cross-linking leads to issues in fragmentation of the DNA to the desired size. As a result, it causes a smaller amount of DNA recovery, requiring the post-ChIP amplification of the yielded DNA.