The Mediator complex as a master regulator of transcription by RNA polymerase II

WF Richter, S Nayak, J Iwasa, DJ Taatjes - Nature Reviews Molecular …, 2022 - nature.com
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits,
controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining …

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 …

GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells

T Zhou, R Zhang, D Jia, RT Doty, AD Munday, D Gao… - Nature …, 2024 - nature.com
The organization of mammalian genomes features a complex, multiscale three-dimensional
(3D) architecture, whose functional significance remains elusive because of limited single …

Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq

Z Liu, Y Chen, Q **a, M Liu, H Xu, Y Chi, Y Deng… - Science, 2023 - science.org
Much progress has been made recently in single-cell chromosome conformation capture
technologies. However, a method that allows simultaneous profiling of chromatin …

Transposable elements in mammalian chromatin organization

HA Lawson, Y Liang, T Wang - Nature Reviews Genetics, 2023 - nature.com
Transposable elements (TEs) are mobile DNA elements that comprise almost 50% of
mammalian genomic sequence. TEs are capable of making additional copies of themselves …

[HTML][HTML] Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration

V Dileep, CA Boix, H Mathys, A Marco, GM Welch… - Cell, 2023 - cell.com
Persistent DNA double-strand breaks (DSBs) in neurons are an early pathological hallmark
of neurodegenerative diseases including Alzheimer's disease (AD), with the potential to …

Long-range enhancer–promoter contacts in gene expression control

S Schoenfelder, P Fraser - Nature Reviews Genetics, 2019 - nature.com
Spatiotemporal gene expression programmes are orchestrated by transcriptional
enhancers, which are key regulatory DNA elements that engage in physical contacts with …

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

H Zheng, W **e - 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 …

Origins of DNA replication in eukaryotes

Y Hu, B Stillman - Molecular cell, 2023 - cell.com
Errors occurring during DNA replication can result in inaccurate replication, incomplete
replication, or re-replication, resulting in genome instability that can lead to diseases such as …