3dgenome
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Initial page
Cover
Preface
Figurelist
Chap0 Preparation
Chap1 Why we care about 3D genome
Chap2 experiment tools for exploring genome interaction
2.1 Image based
2.2 Primary order
2.3 Higher order C-techs
Chap3 Computational analysis
Chap4 RNA-genome interaction
Chap5 Integrative Data Visualization Tools
Chap6 4DN Project
Appendix
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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.)
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.
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2.1 Image based
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Overview:
Primary order structure
Higher order structure