Organization and function of the 3D genome

B Bonev, G Cavalli - Nature Reviews Genetics, 2016 - nature.com
Understanding how chromatin is organized within the nucleus and how this 3D architecture
influences gene regulation, cell fate decisions and evolution are major questions in cell …

Epigenetic control of CD8+ T cell differentiation

AN Henning, R Roychoudhuri, NP Restifo - Nature Reviews …, 2018 - nature.com
Upon stimulation, small numbers of naive CD8+ T cells proliferate and differentiate into a
variety of memory and effector cell types. CD8+ T cells can persist for years and kill tumour …

Heterochromatin drives compartmentalization of inverted and conventional nuclei

M Falk, Y Feodorova, N Naumova, M Imakaev… - Nature, 2019 - nature.com
The nucleus of mammalian cells displays a distinct spatial segregation of active euchromatic
and inactive heterochromatic regions of the genome,. In conventional nuclei, microscopy …

[HTML][HTML] Transcription elongation can affect genome 3D structure

S Heinz, L Texari, MGB Hayes, M Urbanowski… - Cell, 2018 - cell.com
How transcription affects genome 3D organization is not well understood. We found that
during influenza A (IAV) infection, rampant transcription rapidly reorganizes host cell …

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

IM Flyamer, J Gassler, M Imakaev, HB Brandão… - Nature, 2017 - nature.com
Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential
to generate a new organism. The maternal genome inherited from the oocyte and the …

[HTML][HTML] The cohesin release factor WAPL restricts chromatin loop extension

JHI Haarhuis, RH van der Weide, VA Blomen… - Cell, 2017 - cell.com
The spatial organization of chromosomes influences many nuclear processes including
gene expression. The cohesin complex shapes the 3D genome by looping together CTCF …

[HTML][HTML] A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping

SSP Rao, MH Huntley, NC Durand, EK Stamenova… - Cell, 2014 - cell.com
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 …

The selection and function of cell type-specific enhancers

S Heinz, CE Romanoski, C Benner… - Nature reviews Molecular …, 2015 - nature.com
The human body contains several hundred cell types, all of which share the same genome.
In metazoans, much of the regulatory code that drives cell type-specific gene expression is …

The role of chromatin loop extrusion in antibody diversification

Y Zhang, X Zhang, HQ Dai, H Hu, FW Alt - Nature Reviews Immunology, 2022 - nature.com
Cohesin mediates chromatin loop formation across the genome by extruding chromatin
between convergently oriented CTCF-binding elements. Recent studies indicate that …

CTCF: an architectural protein bridging genome topology and function

CT Ong, VG Corces - Nature Reviews Genetics, 2014 - nature.com
The eukaryotic genome is organized in the three-dimensional nuclear space in a specific
manner that is both a cause and a consequence of its function. This organization is partly …