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

In this issue, the editor will bring you about the application of chip_seq in enhancer research. The article is rich in content and analyzed and described from a professional point of view. I hope you can get something after reading this article.

Enhancer is a DNA sequence with the length of tens to thousands of bp in eukaryotic genome, which can significantly improve the transcriptional activity of target genes.

In 1981, Benerji found a 140bp sequence in SV40 DNA, which can greatly improve the expression level of hemoglobin fusion gene, which is located in the upstream of SV40 early gene, and consists of two forward repeat sequences, each of which is in length in 72bp.

Compared with the transcriptional regulation mechanism of the promoter region, the action mode of enhancers has the following characteristics.

With long-distance effect, the distance between enhancer and target gene can be very long, ranging from several K to several M.

Non-directional, enhancers can regulate the target genes on both sides, and the target genes can be on any chain, while the promoter can only downstream nearby genes.

There are many methods to identify enhancers. In the field of chip_seq, the following methods are commonly used.

Peak regions of multiple transcription factors are clustered to identify enhanced subregions.

Two histone modifications, H3K4me1 and K3K27ac, were used as mark enhancers.

POLR2A, the largest subunit of type II RNA polymerase, was used as antibody for chip_seq to recognize enhancers.

Chip_seq using histone acetyltransferase P300 as antibody to recognize enhancers

Through the analysis of chip-seq data, a large number of enhancer sequences were identified. On this basis, the concept of super enhancer is further put forward, and the enrichment region of enhancer is defined as super enhancer. The methods of identification are as follows.

Firstly, the enhanced sub-regions are identified by chip data, and then the enhanced sub-regions are merged, and the enhancers within the range of 12.5kb are merged into one region. Finally, the merged regions and unmerged regions are sorted according to some score, and the diagram of the third step is drawn. The regions with a slope above 1 are called super enhancers.

This is how the application of chip_seq in enhancer research is shared by the editor. If you happen to have similar doubts, you might as well refer to the above analysis to understand. If you want to know more about it, you are welcome to follow the industry information channel.

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