Liquid–liquid phase separation in chromatin

K Rippe - Cold Spring Harbor perspectives in biology, 2022 - cshperspectives.cshlp.org
In eukaryotic cells, protein and RNA factors involved in genome activities like transcription,
RNA processing, DNA replication, and repair accumulate in self-organizing membraneless …

An overview of genome organization and how we got there: from FISH to Hi-C

J Fraser, I Williamson, WA Bickmore… - … and Molecular Biology …, 2015 - Am Soc Microbiol
In humans, nearly two meters of genomic material must be folded to fit inside each
micrometer-scale cell nucleus while remaining accessible for gene transcription, DNA …

HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions

Y Huang, J An, S Sircar, C Bergis, CD Lopes… - Nature …, 2023 - nature.com
The complex and dynamic three-dimensional organization of chromatin within the nucleus
makes understanding the control of gene expression challenging, but also opens up …

Transcription factories: genome organization and gene regulation

A Papantonis, PR Cook - Chemical reviews, 2013 - ACS Publications
All eukaryotic cells contain four RNA polymerases originally defined by their sensitivity to
different drugs, and now by the sets of genes they transcribe. 1− 4 Polymerase I produces …

Retracted article: Detection and replication of epistasis influencing transcription in humans

G Hemani, K Shakhbazov, HJ Westra, T Esko… - Nature, 2014 - nature.com
Epistasis is the phenomenon whereby one polymorphism's effect on a trait depends on other
polymorphisms present in the genome. The extent to which epistasis influences complex …

In the loop: promoter–enhancer interactions and bioinformatics

A Mora, GK Sandve, OS Gabrielsen… - Briefings in …, 2016 - academic.oup.com
Enhancer–promoter regulation is a fundamental mechanism underlying differential
transcriptional regulation. Spatial chromatin organization brings remote enhancers in …

Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations

PR Cook, D Marenduzzo - Nucleic acids research, 2018 - academic.oup.com
Current models for the folding of the human genome see a hierarchy stretching down from
chromosome territories, through A/B compartments and topologically-associating domains …

RNA polymerase II C-terminal domain: tethering transcription to transcript and template

JL Corden - Chemical reviews, 2013 - ACS Publications
By definition the CTD consists of the amino acid sequences extending from the largest
subunit, RPO21 or RPB1 in yeast and POLR2A in human. Specifically the CTD consists of …

The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors

H Wang, B Li, L Zuo, B Wang, Y Yan, K Tian… - Nature …, 2022 - nature.com
Abstract RNA polymerase II (Pol II) apparatuses are compartmentalized into transcriptional
clusters. Whether protein factors control these clusters remains unknown. In this study, we …

Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy

ZW Zhao, R Roy, JCM Gebhardt… - Proceedings of the …, 2014 - National Acad Sciences
Superresolution microscopy based on single-molecule centroid determination has been
widely applied to cellular imaging in recent years. However, quantitative imaging of the …