【三维基因组】loop分析？来先看一篇文献

首先，我们来看一眼文章摘要部分：

We use in situ Hi-C to probe the 3D architecture of genomes, 
constructing haploid and diploid maps of nine cell types. 
The densest, in human lymphoblas-toid cells,
 contains 4.9 billion contacts, achieving 1 kb resolution. 
We find that genomes are partitioned into contact domains (median length, 185 kb), 
which are associated with distinct patterns of histone marks and segregate into six subcompartments. 
We identify ~10,000 loops.
 These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species.
 Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, 
with the asymmetric motifs ‘‘facing’’ one another. 
The inactive X chromosome splits into two massive domains and 
contains large loops anchored at CTCF-binding repeats.

作者对9种细胞系通过原位Hi-C技术捕获其三维结构。其中 人的淋巴细胞共获得了4.9 billion 有效reads数，分辨率达到了1kb，鉴定了～10，000个loop。这些loop往往和enhancer和promoter有关。loop anchor往往富集大量的CTCF结合位点（相向的能达到90%）。