Cis-regulatory sequences in plants: their importance, discovery, and future challenges

RJ Schmitz, E Grotewold, M Stam - The plant cell, 2022 - academic.oup.com
The identification and characterization of cis-regulatory DNA sequences and how they
function to coordinate responses to developmental and environmental cues is of paramount …

Evidence for and against liquid-liquid phase separation in the nucleus

SC Weber - Non-coding RNA, 2019 - mdpi.com
Enclosed by two membranes, the nucleus itself is comprised of various membraneless
compartments, including nuclear bodies and chromatin domains. These compartments play …

The 3D architecture of the pepper genome and its relationship to function and evolution

Y Liao, J Wang, Z Zhu, Y Liu, J Chen, Y Zhou… - Nature …, 2022 - nature.com
The organization of chromatin into self-interacting domains is universal among eukaryotic
genomes, though how and why they form varies considerably. Here we report a …

Phase separation in genome organization across evolution

M Feric, T Misteli - Trends in cell biology, 2021 - cell.com
Phase separation is emerging as a paradigm to explain the self-assembly and organization
of membraneless bodies in the cell. Recent advances show that this principle also extends …

Unraveling the 3D genome architecture in plants: present and future

W Ouyang, D Xiong, G Li, X Li - Molecular Plant, 2020 - cell.com
The eukaryotic genome has a hierarchical three-dimensional (3D) organization with
functional implications for DNA replication, DNA repair, and transcriptional regulation. Over …

3D organization of regulatory elements for transcriptional regulation in Arabidopsis

L Deng, Q Zhou, J Zhou, Q Zhang, Z Jia, G Zhu… - Genome Biology, 2023 - Springer
Background Although spatial organization of compartments and topologically associating
domains at large scale is relatively well studied, the spatial organization of regulatory …

Understanding 3D genome organization and its effect on transcriptional gene regulation under environmental stress in plant: a chromatin perspective

S Kumar, S Kaur, K Seem, S Kumar… - Frontiers in Cell and …, 2021 - frontiersin.org
The genome of a eukaryotic organism is comprised of a supra-molecular complex of
chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal …

Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure

ES Karaaslan, N Wang, N Faiss, Y Liang… - Nature Plants, 2020 - nature.com
Abstract Information in the genome is not only encoded within sequence or epigenetic
modifications, but is also found in how it folds in three-dimensional space. The formation of …

SGF29 nuclear condensates reinforce cellular aging

K Yan, Q Ji, D Zhao, M Li, X Sun, Z Wang, X Liu, Z Liu… - Cell Discovery, 2023 - nature.com
Phase separation, a biophysical segregation of subcellular milieus referred as condensates,
is known to regulate transcription, but its impacts on physiological processes are less clear …

β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture

SR Mahmood, X Xie, N Hosny El Said, T Venit… - Nature …, 2021 - nature.com
Abstract β-actin is a crucial component of several chromatin remodeling complexes that
control chromatin structure and accessibility. The mammalian Brahma-associated factor …