Biology Reference
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A
B
C
D
E
F
DNA-binding
protein
Linker
DNA
Antibody
Figure 10.7 ChIA-PET describes DNA-binding sites and their physical interactions
through DNA looping. The first two steps of ChIA-PET are similar to those of ChIP-
Seq. Briefly, chromatin is cross-linked to stabilize the interactions between its proteins
and DNA components and sonicated (A). Complexes are then purified with a specific
antibody (B). Double stranded linkers containing the binding site of the Mme1 endonu-
clease are ligated to the ends of the fragmented DNA (C). Ligation can occur in cis, when
a DNA fragment is circularized, or in trans, when two different DNA fragments are linked
together (D). After restriction with Mme1, which cuts DNA 27 bp downstream of its bind-
ing site in the genomic fragment (D), the resulting linear fragments are sequenced, pro-
viding paired-end tags (PETs) reflecting the ligation products (E). After mapping to the
reference genome, cis-ligation products are essentially similar to ChIP-Seq end products,
and serve to derive binding profiles and identify DNA-binding sites. Given that the two
tags of trans-ligation products map at distinct genomic locations, they do describe the
network of physical interactions between the DNA-bound proteins (F). All the possible
ligation products are not shown for the sake of simplicity.
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