Basic understanding of ChiA-Pet analysis

Question

[Kritika]

Hi everyone I got one very basic questions so please help me out it may sound silly but please bear with me. I learning ChiA-Pet analysis. I need understanding about wetlab protocol for ChiA-Pet analysis. And how this technique better then other techniques like 3C , chip-seq and hiC

Answer 1

[natasha.sernova]

Comparison of all known approaches:

http://genesdev.cshlp.org/content/26/1/11.full

A decade of 3C technologies: insights into nuclear organization

“Over the past 10 years, the development of chromosome conformation capture (3C) technology and the subsequent genomic variants thereof have enabled the analysis of nuclear organization at an unprecedented resolution and throughput. The technology relies on the original and, in hindsight, remarkably simple idea that digestion and religation of fixed chromatin in cells, followed by the quantification of ligation junctions, allows for the determination of DNA contact frequencies and insight into chromosome topology. Here we evaluate and compare the current 3C-based methods (including 4C [chromosome conformation capture-on-chip], 5C [chromosome conformation capture carbon copy], HiC, and ChIA-PET), summarize their contribution to our current understanding of genome structure, and discuss how shape influences genome function.”

For details of ChIA-PET see this paper(2012):

ChIA-PET analysis of transcriptional chromatin interactions

http://www.sciencedirect.com.sci-hub.cc/science/article/pii/S1046202312002204#

According to Wiki:

https://en.wikipedia.org/wiki/ChIA-PET

“The ChIA-PET method combines ChIP-based methods (Kuo & Allis, 1999), and Chromosome conformation capture (3C), to extend the capabilities of both approaches. ChIP-Sequencing (ChIP-Seq) is a popular method used to identify TFBS while 3C has been used to identify long-range chromatin interactions (Dekker et al., 2002). However, both suffer from limitations when used independently to identify de-novo long-range interactions genome wide. While ChIP-Seq is typically used for genome-wide identification of TFBS (Barski et al., 2007; Wei et al., 2006), it provides only linear information of protein binding sites along the chromosomes (but not interactions between them), and can suffer from high genomic background noise (false positives).”

See their protocol:

http://chiapet.gis.a-star.edu.sg/protocols

This is a relatively recent article:

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-S12-S11

And one more, even younger:

Mango: A bias correcting ChIA-PET analysis pipeline

http://bioinformatics.oxfordjournals.org/content/early/2015/06/01/bioinformatics.btv336

Soft: 3C/4C/5C/Hi-C/ChIA-PET sequencing software tools

High-throughput sequencing software tools

https://omictools.com/3c-4c-5c-hi-c-chia-pet-category