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 lymphoblastoid cells, contains 4.9 billion …

Hi-C experiments explore the 3D structure of the genome, generating terabases of data to
create high-resolution contact maps. Here, we introduce Juicer, an open-source tool for …

We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes.
Here, we combine these maps with new Hi-C, microscopy, and genome-editing …

The human genome folds to create thousands of intervals, called "contact domains," that
exhibit enhanced contact frequency within themselves. "Loop domains" form because of …

Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian
genomes. However, extrusion has not been visualized in vivo, and thus, its functional …

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional
(3D) genome architectures at the chromosome scale. Each type appears and …

In this study, we show that evolutionarily conserved chromosome loop anchors bound by
CCCTC-binding factor (CTCF) and cohesin are vulnerable to DNA double strand breaks (DSBs…

Chromosome organization is crucial for genome function. Here, we present a method for
visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce …

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing
depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally …

While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism
of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and …