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

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。

f-1

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。

f-2

hi-c 文献导读-2 TAD