<p>Hi all,</p>

<p>To my understanding, in the ChiA-PET method we:  </p>

<ul>
<li>Use formaldehyde to capture the cross-linking of the chromatin</li>
<li>Digest the chromatin</li>
<li>In general, ligate the chromatin strands to create pet samples</li>
</ul>

<p>And in the Hi-C method we perform pretty much the same.</p>

<p>The end result of both should be information on chromatin interactions, so:</p>

<ul>
<li>What is the basic difference between the process of ChiA-PET and Hi-C methods?</li>
<li>What is the difference in the result of the methods?</li>
</ul>

<p>Thanks</p>

<p>I'm not an expert in either, but my understanding is that ChiA-PET is generally a more powerful method in that (1) it allows you to probe long-distance interactions relevant to some protein of interest, (2) it involves ligation of known adapters containing Mme1 cut-sites, which are exploited to get fragments with both sides of an interaction separated by known sequence, and (3) you can use multiple adapter sequences with ChiA-PET (divide the initial cross-linked and sonicated sample into multiple tubes) to gauge how frequently false-positives are found. In my mind, points 1 and 3 are big selling points, but there may be other big differences. There's a nice visual comparison of the two in figure 4 of <a href='http://www.annualreviews.org/doi/pdf/10.1146/annurev-genom-090711-163818'>this review article</a>.</p>
