Organizational principles of 3D genome architecture

MJ Rowley, VG Corces - Nature Reviews Genetics, 2018 - nature.com
Studies of 3D chromatin organization have suggested that chromosomes are hierarchically
organized into large compartments composed of smaller domains called topologically …

The relationship between genome structure and function

AM Oudelaar, DR Higgs - Nature Reviews Genetics, 2021 - nature.com
Precise patterns of gene expression in metazoans are controlled by three classes of
regulatory elements: promoters, enhancers and boundary elements. During differentiation …

Mitochondrial base editor induces substantial nuclear off-target mutations

Z Lei, H Meng, L Liu, H Zhao, X Rao, Y Yan, H Wu… - Nature, 2022 - nature.com
DddA-derived cytosine base editors (DdCBEs)—which are fusions of split DddA halves and
transcription activator-like effector (TALE) array proteins from bacteria—enable targeted C• …

Eukaryotic core promoters and the functional basis of transcription initiation

V Haberle, A Stark - Nature reviews Molecular cell biology, 2018 - nature.com
Abstract RNA polymerase II (Pol II) core promoters are specialized DNA sequences at
transcription start sites of protein-coding and non-coding genes that support the assembly of …

Predicting 3D genome folding from DNA sequence with Akita

G Fudenberg, DR Kelley, KS Pollard - Nature methods, 2020 - nature.com
In interphase, the human genome sequence folds in three dimensions into a rich variety of
locus-specific contact patterns. Cohesin and CTCF (CCCTC-binding factor) are key …

[HTML][HTML] YY1 is a structural regulator of enhancer-promoter loops

AS Weintraub, CH Li, AV Zamudio, AA Sigova… - Cell, 2017 - cell.com
There is considerable evidence that chromosome structure plays important roles in gene
control, but we have limited understanding of the proteins that contribute to structural …

Cohesin loss eliminates all loop domains

SSP Rao, SC Huang, BG St Hilaire, JM Engreitz… - Cell, 2017 - cell.com
The human genome folds to create thousands of intervals, called" contact domains," that
exhibit enhanced contact frequency within themselves." Loop domains" form because of …

The structural basis for cohesin–CTCF-anchored loops

Y Li, JHI Haarhuis, Á Sedeño Cacciatore… - Nature, 2020 - nature.com
Cohesin catalyses the folding of the genome into loops that are anchored by CTCF. The
molecular mechanism of how cohesin and CTCF structure the 3D genome has remained …

Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization

EP Nora, A Goloborodko, AL Valton, JH Gibcus… - Cell, 2017 - cell.com
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly
understood. The transcription factor CTCF is a candidate regulator of chromosomal …

Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression

B Van Steensel, AS Belmont - Cell, 2017 - cell.com
In metazoan cell nuclei, hundreds of large chromatin domains are in close contact with the
nuclear lamina. Such lamina-associated domains (LADs) are thought to help organize …