Three-dimensional genome architecture: players and mechanisms

A Pombo, N Dillon - Nature reviews Molecular cell biology, 2015 - nature.com
The different cell types of an organism share the same DNA, but during cell differentiation
their genomes undergo diverse structural and organizational changes that affect gene …

Genome-wide map** and analysis of chromosome architecture

AD Schmitt, M Hu, B Ren - Nature reviews Molecular cell biology, 2016 - nature.com
Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in
the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects …

Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element

SW Cho, J Xu, R Sun, MR Mumbach, AC Carter… - Cell, 2018 - cell.com
Noncoding mutations in cancer genomes are frequent but challenging to interpret. PVT1
encodes an oncogenic lncRNA, but recurrent translocations and deletions in human cancers …

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

R Stadhouders, E Vidal, F Serra, B Di Stefano… - Nature …, 2018 - nature.com
Chromosomal architecture is known to influence gene expression, yet its role in controlling
cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem …

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

J Zuin, JR Dixon, MIJA Van Der Reijden, Z Ye… - Proceedings of the …, 2014 - pnas.org
Recent studies of genome-wide chromatin interactions have revealed that the human
genome is partitioned into many self-associating topological domains. The boundary …

Obesity-associated variants within FTO form long-range functional connections with IRX3

S Smemo, JJ Tena, KH Kim, ER Gamazon, NJ Sakabe… - Nature, 2014 - nature.com
Genome-wide association studies (GWAS) have reproducibly associated variants within
introns of FTO with increased risk for obesity and type 2 diabetes (T2D),,. Although the …

Enhancer release and retargeting activates disease-susceptibility genes

S Oh, J Shao, J Mitra, F **ong, M D'Antonio, R Wang… - Nature, 2021 - nature.com
The functional engagement between an enhancer and its target promoter ensures precise
gene transcription. Understanding the basis of promoter choice by enhancers has important …

Genome-wide characterization of mammalian promoters with distal enhancer functions

LTM Dao, AO Galindo-Albarrán… - Nature …, 2017 - nature.com
Gene expression in mammals is precisely regulated by the combination of promoters and
gene-distal regulatory regions, known as enhancers. Several studies have suggested that …

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

JR Hughes, N Roberts, S McGowan, D Hay… - Nature …, 2014 - nature.com
Gene expression during development and differentiation is regulated in a cell-and stage-
specific manner by complex networks of intergenic and intragenic cis-regulatory elements …