3dgenome
  • Initial page
  • Cover
  • Preface
  • Figurelist
  • Chap0 Preparation
    • 0.1 Molecular biology
    • 0.2 Sequencing technologies
    • 0.3 RNA-seq Data Mapping & Gene Quantification
    • 0.4 RNA-seq Differential Analysis
  • Chap1 Why we care about 3D genome
    • 1.1 From 2D to 3D nuclear structure
    • 1.2 From static to dynamic
    • 1.3 From intra to inter chromosomes "talk"
    • 1.4 From aggregation to division - phase separation
  • Chap2 experiment tools for exploring genome interaction
    • 2.1 Image based
    • 2.2 Primary order
    • 2.3 Higher order C-techs
  • Chap3 Computational analysis
    • 3.1 Primary order analysis
    • 3.2 Higer order data analysis
      • 3.2.1 Read mapping consideration
      • 3.2.2 Analytical Pipelines
        • GITAR Pipeline
        • HiC-Pro Pipeline
      • 3.2.3 TAD calling algorithms
    • 3.3 3D structure
  • Chap4 RNA-genome interaction
    • 4.1 Experimental Methods
    • 4.2 Computational Analysis
  • Chap5 Integrative Data Visualization Tools
    • 5.1 GIVE
    • 5.2 HiGlass
  • Chap6 4DN Project
  • Appendix
    • Homework
    • Student's presentation
      • A Brief Introduction to Machine Learning
      • Precision medicine
      • CHIP-Seq
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  • Overview:
  • Primary order structure
  • Higher order structure

Chap2 experiment tools for exploring genome interaction

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Last updated 6 years ago

Overview:

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 .

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Figure1 Experimental tools for primary and higher order genome interaction (Risca, V. I.et al.Trends in Genetics 31.7(2015):357-372.)