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 …

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 …

Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits

C Sun, J Huang, Y Wang, X Zhao, L Su… - Molecular biology …, 2021 - academic.oup.com
Bumblebees are a diverse group of globally important pollinators in natural ecosystems and
for agricultural food production. With both eusocial and solitary life-cycle phases, and some …

Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation

D Lin, W Xu, P Hong, C Wu, Z Zhang, S Zhang… - Nature …, 2022 - nature.com
Immunocytes dynamically reprogram their gene expression profiles during differentiation
and immunoresponse. However, the underlying mechanism remains elusive. Here, we …

Chromatin conformation analysis of primary patient tissue using a low input Hi-C method

N Díaz, K Kruse, T Erdmann, AM Staiger, G Ott… - Nature …, 2018 - nature.com
Chromatin conformation constitutes a fundamental level of eukaryotic genome regulation.
However, our ability to examine its biological function and role in disease is limited by the …

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 …

Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation

L Zhao, S Wang, Z Cao, W Ouyang, Q Zhang… - Nature …, 2019 - nature.com
Insight into high-resolution three-dimensional genome organization and its effect on
transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach …

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 …

3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize

Y Sun, L Dong, Y Zhang, D Lin, W Xu, C Ke, L Han… - Genome biology, 2020 - Springer
Background Maize ears and tassels are two separate types of inflorescence which are
initiated by similar developmental processes but gradually develop distinct architectures …

Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure

Y Hou, F Li, R Zhang, S Li, H Liu, ZS Qin, X Sun - Epigenetics, 2019 - Taylor & Francis
ABSTRACT DNA molecules are highly compacted in the eukaryotic nucleus where distal
regulatory elements reach their targets through three-dimensional chromosomal …