ChIP-seq combat | chromatin co-immunoprecipitation technology | ATAC-seq | chromatin open sequencing technology

Reference: Shengxin Skill Tree

Overview of ChIP-Seq

Some simple copies are purely personal notes. 

 

Principles of ChIP-seq

Techniques for the genome-wide study of DNA-binding proteins (interactions), histone modifications (epigenetic marks), and nucleosomes, three topics that contribute to understanding the interregulation of genes and chromosomes functional structure.

Under physiological conditions, the cells are lysed after crosslinking the DNA and proteins in the cells, the chromosomes are separated, the chromatin is randomly cut by ultrasound or enzyme treatment, and the specific recognition reaction of antigen and antibody is used to combine with the target protein. The DNA fragments are precipitated, and then the DNA fragments bound to the protein are released by reverse crosslinking, and finally the sequences of the DNA fragments are obtained by sequencing.

First lock DNA and protein, cleavage, enrich specific DNA with antigen, unlock DNA and protein, and get the DNA fragment we want for sequencing analysis.

 

 

ATAC-seq | Chromatin Open Sequencing Technology

Reference: ATAC-seq: Open Chromatin Sequencing Technology

The full name of ATAC-seq is Assay for Transposase Accessible Chromatin with high-throughput sequencing, which is a high-throughput sequencing technology that uses transposase to study chromatin accessibility.

DNA transposition is a phenomenon in which the DNA sequence is transferred from one region of the chromosome to another region, which is realized by DNA transposase. This kind of transposition insertion into DNA also requires that the chromatin at the insertion site is open, otherwise it will be stuck by a large pile of high-level structures.

The results obtained by ATAC-seq have strong consistency with the results obtained by traditional methods, and also have a high degree of agreement with ChIP-seq based on histone modification markers. That is to say, peaks in ATAC-seq are often promoters, enhancer sequences, and binding sites for some trans-regulatory factors.

Is the transposase Tn5 selective for DNA sequence? I think it should be no, otherwise this method is only sensitive to a specific sequence.

 

 

To be continued~