Shulou(Shulou.com)06/01 Report--

Today, I will talk to you about the example analysis of Chip-seq. Many people may not know much about it. In order to make you understand better, the editor has summarized the following for you. I hope you can get something according to this article.

Chromatin co-precipitation technique can be used to study the interaction between DNA and protein in vivo. Firstly, the DNA-protein binding complex is immobilized in living cells, then the complex is captured by protein-specific antibody by immunological means of antigen-antibody specific binding, and then the protein is eluted to obtain the DNA fragment bound to the target protein. The enriched DNA fragment is sequenced on the computer. That is, the formation of a mature analysis process, called chip-seq, which combines traditional chip technology with high-throughput sequencing, corresponding to the following English

Chromatin immunoprecipitation followed by sequencing

Relying on the development of high-throughput sequencing and bioinformatics analysis, Chip-seq technology can analyze the interaction between DNA and proteins in the whole genome. at present, it is often used to study transcription factors and the binding sites of various histone modifications on the genome. compared with chip-based Chip-chip technology, chip-seq has a shorter experimental cycle, more efficient and covers a wider range of genomes. With the decrease of sequencing price, chip-seq has become one of the powerful tools to study gene regulation and epigenetic modification.

The experimental process is as follows

In the whole experimental process, the core is to select the specific antibody according to the research object. The higher the specificity and sensitivity of the antibody, the better the enrichment effect of the corresponding DNA sequence, the easier to detect the binding region.

For chip-seq data analysis, the core is to detect the location of the enriched DNA on the genome called peak. The schematic diagram of the analysis is as follows.

Theoretically speaking, the sequence depth of the enriched DNA on the genome will be relatively high, and these regions can be found by analyzing the distribution of sequence depth on the genome. In the actual construction of the database, due to the uneven distribution of fragments, there will be some non-specific binding sites with similar peak patterns, that is, it is necessary to find the real protein binding sites by setting control samples and with the help of mature bioinformatics analysis software, and the step of finding DNA binding sites is called peak calling.

After the completion of the peak calling, you need to annotate the peak. There are two kinds of annotations. The first is to analyze which functional regions peak is located in, such as promoter region, exon region, intron region and so on. The most typical transcription factor is usually located in the promoter region of the gene. The second kind of annotation is the annotation of adjacent genes. After the protein binds to DNA, it mainly plays the role of gene expression regulation, and the adjacent genes of these peak regions are used as candidate regulatory genes.

At the same time, these peak regions can be analyzed by motif to identify the conserved sites of protein binding.

Of course, we can also combine different experimental conditions to analyze the difference of DNA binding ability among case/control groups, so as to analyze the effect of experimental conditions on protein binding ability.

After reading the above, do you have any further understanding of the example analysis of Chip-seq? If you want to know more knowledge or related content, please follow the industry information channel, thank you for your support.

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