The spatial organization of transcriptional control

A Hafner, A Boettiger - Nature Reviews Genetics, 2023 - nature.com
In animals, the sequences for controlling gene expression do not concentrate just at the
transcription start site of genes, but are frequently thousands to millions of base pairs distal …

Understanding 3D genome organization by multidisciplinary methods

I Jerkovic, G Cavalli - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …

[HTML][HTML] A human brain vascular atlas reveals diverse mediators of Alzheimer's risk

AC Yang, RT Vest, F Kern, DP Lee, M Agam, CA Maat… - Nature, 2022 - nature.com
The human brain vasculature is of great medical importance: its dysfunction causes
disability and death, and the specialized structure it forms—the blood–brain barrier …

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

A Nott, IR Holtman, NG Coufal, JCM Schlachetzki, M Yu… - Science, 2019 - science.org
Noncoding genetic variation is a major driver of phenotypic diversity, but functional
interpretation is challenging. To better understand common genetic variation associated with …

Methods for mapping 3D chromosome architecture

R Kempfer, A Pombo - Nature Reviews Genetics, 2020 - nature.com
Determining how chromosomes are positioned and folded within the nucleus is critical to
understanding the role of chromatin topology in gene regulation. Several methods are …

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

N Kubo, H Ishii, X Xiong, S Bianco… - Nature structural & …, 2021 - nature.com
The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive the
formation of chromatin loops and topologically associating domains, but its role in gene …

EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps

X Wang, Y Luan, F Yue - Science Advances, 2022 - science.org
The Hi-C technique has been shown to be a promising method to detect structural variations
(SVs) in human genomes. However, algorithms that can use Hi-C data for a full-range SV …

UTX condensation underlies its tumour-suppressive activity

B Shi, W Li, Y Song, Z Wang, R Ju, A Ulman, J Hu… - Nature, 2021 - nature.com
UTX (also known as KDM6A) encodes a histone H3K27 demethylase and is an important
tumour suppressor that is frequently mutated in human cancers. However, as the …

The role of 3D genome organization in development and cell differentiation

H Zheng, W Xie - Nature reviews Molecular cell biology, 2019 - nature.com
In eukaryotes, the genome does not exist as a linear molecule but instead is hierarchically
packaged inside the nucleus. This complex genome organization includes multiscale …

Circular ecDNA promotes accessible chromatin and high oncogene expression

S Wu, KM Turner, N Nguyen, R Raviram, M Erb… - Nature, 2019 - nature.com
Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in
cancer,, but our understanding of the structure of ecDNA and its effect on gene regulation is …