Comparing DAP-Seq vs Chip-Seq
ChIP-Seq
|
DAP-Seq
|
|
Common
|
w Detecting
DNA binding proteins with sequencing technique
w As
they are using sequencing technique there are several advantages compared to protein
binding array
- Array
needs primary sequence to make a probe
- Array
is hard to find tissue-specific 5-methylcytosine
|
|
Goal
|
w Histone
modifications O
e.g.
H3Kme1 - (epigenetic modification to histone)
w Transcription
factors O
|
w Histone
modifications X
w Transcription
factors O
|
TF-DNA
binding
|
w In
vivo
w Formaldehyde
fixation(cross link)
|
w In
vitro
w Affinity
purified TF - gDNA
(but not nucleosome-disadvantages)
|
Antibody
|
w Using
Antibody
- Sometimes
hard to execute because of antibody quality. As antibody is sensitive with heat.
- Require
specific antibody. It can take years to develop the new antibody.
w Need
input (Nonspecific antibody) to accurately normalize data
|
w X
Antibody
|
Lowly
expressed protein
|
w Hard
to detect. Because protein(antibody) is hard to be detected.
|
w Easy
to detect
|
Background
Noise
| w Yes (need negative control) | w Yes (need negative control) |
Pipeline
(statistic)
|
w Peak
calling – MACS
- Find
the peak: sample vs Input(control)
|
w GEM
peak caller(O’Mally 2016)
|
In common, Chip-Seq and DAP-Seq can detect the DNA binding proteins such as transcription factor binding site. Then what is transcription factor?
Transcription factor
regulates the transcription (DNA->mRNA). When the gene is expressed, the
general transcription factors bind to promotor.
ChIP-Seq(Chromatin
Immunoprecipitation) is well known technique to find the region attached with
transcription factors. In ChIP-Seq,
