# Chap2 experiment tools for exploring genome interaction

## Overview:

![ Figure1 Experimental tools for primary and  higher order genome interaction (Risca, V. I.et al.Trends in Genetics 31.7(2015):357-372.)](https://2185211125-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LHa3gDECHFHyklI99-v%2F-LHcBrYDCrvN0COsRfA-%2F-LHcCqobTIvInX6ATcJK%2Foverview.JPG?alt=media\&token=66aa728d-493a-44e5-b873-888c731592ef)

Just like the complex structure of one functional protein, a chromosome also has a wired, compacted structure that is flexible during the process of life. Chromatin is a highly compact and organized assembly of DNA and proteins. From a naked single molecular to a visible chromosome, DNA in mammalian is condensed approximately 10,000 to 20,000-fold. We will introduce the experimental tools from two category: “higher-order” and “primary-order” structure of chromosomal DNA according to the folding complexity.

### Primary order structure

The primary-order chromatin refers to the unpacked chromatin fiber where 11-nm coils of nucleosomes are exposed. The nucleosome is the fundamental unit of chromatin and is represented as a beads-on-the-string model.

### Higher order structure

The higher-order genome structure is most clearly visible during the interphase and mitosis when chromatin fibers extensively fold into chromosomes. An interphase chromosome is formed by a tightly coiled 250 nm chromatid. Microscopic imaging has demonstrated that each chromosome may be confined to genomic compartments. Within these compartments, intra-chromosomal interactions are most frequent within regions known as megabase-sized topologically associ- ating domains (TADs). The active TADs are rich in genes, open chroma- tin marks, transcription factors and DNase I-hypersensitive sites (DHSs) and show early replication. In contrast, the inactive TADs harbor few genes and DHSs and show late replication [1](https://doi.org/10.1016/j.csbj.2018.02.003).