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

This article introduces you how to understand chromatin loops chromatin, the content is very detailed, interested friends can refer to, hope to be helpful to you.

Using the Hi-C genome interaction map with 5kb resolution, the scientists identified the chromatin structure of chromatin loop.

Through the analysis of different resolution Hi-C patterns, different levels of chromatin structure were detected, and the order from high to low was A big B compartments, subcompartments, TAD, chromation loop. The corresponding relationship between Hi-C map and chromatin structure model is as follows

In the early study, using the Hi-C map of 1MB, it was defined that each chromatin contained An and B compartments. In this paper, based on the cluster analysis of the HI-C map of 100kb resolution, it is found that the A _ big B compartments is further divided into six subgroups, namely subcompartments. Based on the cluster analysis of each Hi-C map of chromatin, 5 cluster were obtained except for chromatin 19, and 6 cluster for chromatin 19.

By analyzing the relationship between these subcompartments and A compartments B, it was found that 2 of them belonged to A compartments, labeled A1 and A2, and the other 4 belonged to B comprtmants, labeled B1, B2, B3, B4.

For the identification of TAD topological association domains, an ArrowHead algorithm is created, the core of which is to transform the normalized interaction matrix. The changing formula is as follows.

Similar to DI's algorithm, iMurd and ibin represent two upstream and downstream bin, respectively. If the interaction frequency between I and upstream bin is high, the A value is positive, if the interaction frequency with downstream bin is high, the A value is negative, and if equal, it is 0. The hint is as follows

The square area in figure An is a TAD domain, which is transformed into the shape shown in figure B. Corresponding to the entire interaction matrix, it looks like the arrow shown in figure E. By using the dynamic programming algorithm, the arrow region in the transformed matrix can be identified and the TAD domain can be predicted. The length of the TAD domain identified in this article is 40kb-3Mb, and the median is 185kb.

For the chromatin ring, it is defined as the lattice region in the Hi-C map with higher interaction frequency than the surrounding adjacent regions, such a region is called peak, and the corresponding chromatin region is called peak loci, which is marked by blue dots in the following figure.

As shown in the image above, the peak region is identified by comparing the interaction frequency with the surrounding area, which requires that the resolution of the HI-C map is below 5kb. For the genome-wide interaction map, the amount of computation is very large. The author also provides an algorithm called HiCCUPS, which is integrated into the developed juicer software.

The chromatin ring regions of different cell lines and different species are further compared. The results are as follows.

It was found that it was relatively stable among different cell lines and evolutionarily conservative among species. Based on the analysis of the distribution position of chromatin ring, it was found that it was at the boundary of TAD. Further analysis found that a large part of the chromatin ring is promoter-enhancer loops, which also explains the regulatory mechanism of the enhancer to the target gene. Although the enhancer is linearly distant from the target gene, the enhancer and the target gene promoter are located on a chromatin ring and are close in space, and regulate the target gene by combining with the promoter.

Various mark enriched in the corresponding region of the chromatin ring were analyzed, and it was found that they were rich in transcription factors such as CTCF, as shown in the following figure.

For the spatial structure of chromatin ring, the following model is proposed.

The chromatin ring, a chromatin structural unit, can be identified by constructing a Hi-C map with a resolution below 5kb.

On how to understand chromatin loops chromatin to share here, I hope that the above content can be of some help to you, can learn more knowledge. If you think the article is good, you can share it for more people to see.

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.