Mammalian chromosomes are organized at different length scales within the cell nucleus.
Topologically Associating Domains (TADs) are structural units of 3D genome organization …

How enhancers activate their distal target promoters remains incompletely understood. Here
we dissect how CTCF-mediated loops facilitate and restrict such regulatory interactions …

Over the past decade, genome-wide assays for chromatin interactions in single cells have
enabled the study of individual nuclei at unprecedented resolution and throughput. Current …

The field of 3D genome organization produces large amounts of sequencing data from Hi-C
and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive …

Loop-extrusion and phase-separation have been proposed as mechanisms that shape
chromosome spatial organization. It is unclear, however, how they perform relative to each …

Leukemias with ambiguous lineage comprise several loosely defined entities, often without
a clear mechanistic basis. Here, we extensively profile the epigenome and transcriptome of …

Eukaryotic genomes are organized in 3D in a multiscale manner, and different mechanisms
acting at each of these scales can contribute to transcriptional regulation. However, the large …

Abstract Changes in gene regulation were a major driver of the divergence of archaic
hominins (AHs)—Neanderthals and Denisovans—and modern humans (MHs). The three …

Transcriptional control by distal enhancers is an integral feature of gene regulation. To
understand how enhancer-promoter interactions arise and assess the impact of disrupting …

Eviction of histones from nucleosomes and their exchange with newly synthesized or
alternative variants is a central epigenetic determinant. Here, we define the genome-wide …