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The purpose of this article is to share with you how to carry out A compartment B: chromatin compartment analysis. The editor thinks it is very practical, so I share it with you. I hope you can get something after reading this article. Let's take a look at it.

The emergence of Hi-C technology has promoted the development of three-dimensional genomics. Using Hi-C technology, scientists have not only confirmed the existence of chromatin territory, but also further discovered more three-dimensional characteristics of chromatin.

Lieberman-Aiden et al. studied the three-dimensional structure of human lymphoblasts by Hi-C technique, and put forward the concept of Ahand B compartment for the first time.

Construct the genome interaction map at 1Mb resolution, then use Oberved/Expected 's algorithm to normalize the interaction matrix, and calculate the Poisson correlation coefficient for the normalized matrix. The heat map corresponding to the matrix is shown below.

In the normalized interaction matrix heat map, blue represents that the observed interaction frequency is less than the expected interaction frequency, and red indicates that the observed interaction frequency is greater than the expected interaction frequency. In the heat map of the correlation coefficient matrix, the correlation coefficient ranges from-1 to 1, and the color transitions from blue to red.

According to the PCA dimensionality reduction analysis of the correlation coefficient matrix, the chromatin region can be clearly divided into two parts on the first principal component PC1 axis, which is called A _ compartment B compartment. Corresponding to the positive and negative parts of Eigenvector in the following figure

Through the study of gene expression, histone modification and DNase enzyme hypersensitive sites corresponding to positive and negative regions, it is found that there are more genes in positive regions, the corresponding gene expression is relatively high, and the signals of H3K36me3 and DNA hypersensitive sites are also relatively high. These characteristics indicate that these regions are more open, accessible, transcriptional activated regions. This region is defined as A compartment, which corresponds to the open chromatin region. However, the negative corresponding region contains a small number of genes and low content, so it is defined as B compartment, corresponding to the closed chromatin region.

The above is how to carry out A compartment B: chromatin compartment analysis, the editor believes that there are some knowledge points that we may see or use in our daily work. I hope you can learn more from this article. For more details, please follow the industry information channel.

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