Unraveling the 3D Genome Architecture in Plants: Present and Future.

IF: 21.949

Cited by: 42

Abstract

The eukaryotic genome has a hierarchical three-dimensional (3D) organization with functional implications for DNA replication, DNA repair, and transcriptional regulation. Over the past decade, scientists have endeavored to elucidate the spatial characteristics and functions of plant genome architecture using high-throughput chromatin conformation capturing technologies such as Hi-C, ChIA-PET, and HiChIP. Here, we systematically review current understanding of chromatin organization in plants at multiple scales. We also discuss the emerging opinions and concepts in 3D genome research, focusing on state-of-the-art 3D genome techniques, RNA-chromatin interactions, liquid-liquid phase separation, and dynamic chromatin alterations. We propose the application of single-cell/single-molecule multi-omics, multiway (DNA-DNA, DNA-RNA, and RNA-RNA interactions) chromatin conformation capturing methods, and proximity ligation-independent 3D genome-mapping technologies to explore chromatin organization structure and function in plants. Such methods could reveal the spatial interactions between trait-related SNPs and their target genes at various spatiotemporal resolutions, and elucidate the molecular mechanisms of the interactions among DNA elements, RNA molecules, and protein factors during the formation of key traits in plants.

Keywords

MERFISH

Omics

3D genomic methods

RNA–chromatin interaction

dynamic chromatin organization

liquid–liquid phase separation

plant 3D genome

MeSH terms

Chromatin

Genome, Plant

Imaging, Three-Dimensional

Nucleic Acid Conformation

Plants

RNA, Plant

Authors

Ouyang, Weizhi

Xiong, Dan

Li, Guoliang

Li, Xingwang

Recommend literature

1. Chromatin Tracing: Imaging 3D Genome and Nucleome.

2. Developing novel methods to image and visualize 3D genomes.

3. Single-cell imaging of genome organization and dynamics.

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

5. Higher-Order Chromatin Organization Using 3D DNA Fluorescent In Situ Hybridization.

Similar data

1. Reorganization of 3D chromatin architecture of rice genomes during heat stress (ATAC-Seq)

2. Reorganization of 3D chromatin architecture of rice genomes during heat stress (HiC)

3. Reorganization of 3D chromatin architecture of rice genomes during heat stress (RNA-Seq)

4. Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_Hi-C)

5. Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_ATAC)