• 文献：Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions
• PubMed ID：22495300
• GEO：GSE35156
• 关键字：TAD

1、data processing

1.1 细胞类型

（1） pluripotent cells

• mouse embryonic stem cells (mESCs); 小鼠胚胎干细胞
• human embryonic stem cells (hESCs)；人胚胎干细胞

（2）differentiated cells

• human IMR90 fibroblasts. 人IMR90成纤维细胞
• the mouse cortex 小鼠大脑皮层细胞

1.2 步骤

（1）hi-c 测序，共得到1.7 billion read pairs
（2）normalized the Hi-C interactions for biases in the data
（3）validate the quality of our Hi-C data
（4）visualized 2D-interaction matrices using a variety of bin sizes

2、Topological domains

2.1 finding

• 前提：at bin sizes less than 100kb

• 特征：
  （1）highly self-interacting regions；
  （2）bounded by narrow segments( boundary regions) where thechromatin interactions appear to end abruptly；
  （3） “triangles” on the heatmap

  
  2.1

2.2 characterization

（1）鉴定依据

• DI (directionality index)
  quantify the degree of upstream or downstream interaction bias for a genomic region, which varies considerably at the periphery of the topological domains.

  
  2.2-1

然后使用HMM算法，基于DI指标，infer the locations of topological domains in the genome，最后推算 2,200 topological domains in mESCs with a median size of 880kb that occupy ~91% of the genome .

2.2-2

（2）interactions

• the frequency of intra-domain interactions is higher than inter-domain interactions；
• probes in the same topological domain are closer in nuclear space than probes in different topological domains.

2.2-3

（3） topological boundary regions

• might correspond to insulator or barrier elements.
  研究表明HoxA locus is separated into two compartments by an experimentally validated insulator ；这在boundary regions也发现了

  
  2.2-4

• a strong enrichment of CTCF ：classical insulators

  
  2.2-5

• examined the distribution of the H3K9me3(heterochromatin mark) in humans and mice in relation to the topological domains

• Taken together, the above observations strongly suggest that the topological domain boundaries correlate with regions of the genome displaying classical insulator and barrier element activity

• We have identified multiple factors that are associated with the boundary regions separating topological domains, including the insulator binding factor CTCF, housekeeping genes,SINE elements.

  
  2.2-6

2.3 统一性

（1）between cell types

• In both human and mouse, the majority of the boundary regions are shared between cell types；
• the overall domain structure between cell types is largely unchanged.

2.3-1

• Dynamic interacting regions are enriched for differentially expressed genes
• Therefore, we favor a model where the domain organization is stable between cell types, but the regions within each domain may be dynamic, potentially taking part in cell-type specific regulatory events.

（2）between species(across evolution)

• compared the domain boundaries between mouse ES cells and human ES cells;

• 结果：53.8% of human boundaries are boundaries in mouse and 75.9% of mouse boundaries are boundaries in humans.

  
  2.3-2
• 结论：The syntenic regions in mouse and human in particular share a high degree of similarity in their higher order chromatin structure, indicating that there is conservation of genomic structure beyond the primary sequence of DNA.

2.3-3

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其他教程相关附图
1、当Hi-C分辨率到达10kb时，我们会发现多个相关连loop组成的拓扑相关结构域（TADs）。且TADs边界上一般都会有CTCF的富集。

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2、当分辨率到达50kb时，我们可以看到由相关TADs组成的染色质区域。
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