Spatial Features and Functional Implications of Plant 3D Genome Organization

Katherine Domb; Nan Wang; Guillaume Hummel; Chang Liu

doi:10.1146/annurev-arplant-102720-022810

Spatial Features and Functional Implications of Plant 3D Genome Organization

Katherine Domb, Nan Wang, Guillaume Hummel, Chang Liu^*

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

Abstract

The advent of high-throughput sequencing-based methods for chromatin conformation, accessibility, and immunoprecipitation assays has been a turning point in 3D genomics. Altogether, these new tools have been pushing upward the interpretation of pioneer cytogenetic evidence for a higher order in chromatin packing. Here, we review the latest development in our understanding of plant spatial genome structures and different levels of organization and discuss their functional implications. Then, we spotlight the complexity of organellar (i.e., mitochondria and plastids) genomes and discuss their 3D packing into nucleoids. Finally, we propose unaddressed research axes to investigate functional links between chromatin-like dynamics and transcriptional regulation within organellar nucleoids.

Original language	English
Pages (from-to)	173-200
Number of pages	28
Journal	Annual Review of Plant Biology
Volume	73
DOIs	https://doi.org/10.1146/annurev-arplant-102720-022810
State	Published - 2022
Externally published	Yes

Keywords

3D genomes
TADs
chromatin
nucleoids
organelles
polyploidy
topologically associated domains

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10.1146/annurev-arplant-102720-022810

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abstract = "The advent of high-throughput sequencing-based methods for chromatin conformation, accessibility, and immunoprecipitation assays has been a turning point in 3D genomics. Altogether, these new tools have been pushing upward the interpretation of pioneer cytogenetic evidence for a higher order in chromatin packing. Here, we review the latest development in our understanding of plant spatial genome structures and different levels of organization and discuss their functional implications. Then, we spotlight the complexity of organellar (i.e., mitochondria and plastids) genomes and discuss their 3D packing into nucleoids. Finally, we propose unaddressed research axes to investigate functional links between chromatin-like dynamics and transcriptional regulation within organellar nucleoids.",

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AU - Wang, Nan

AU - Hummel, Guillaume

AU - Liu, Chang

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AB - The advent of high-throughput sequencing-based methods for chromatin conformation, accessibility, and immunoprecipitation assays has been a turning point in 3D genomics. Altogether, these new tools have been pushing upward the interpretation of pioneer cytogenetic evidence for a higher order in chromatin packing. Here, we review the latest development in our understanding of plant spatial genome structures and different levels of organization and discuss their functional implications. Then, we spotlight the complexity of organellar (i.e., mitochondria and plastids) genomes and discuss their 3D packing into nucleoids. Finally, we propose unaddressed research axes to investigate functional links between chromatin-like dynamics and transcriptional regulation within organellar nucleoids.

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KW - TADs

KW - chromatin

KW - nucleoids

KW - organelles

KW - polyploidy

KW - topologically associated domains

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JO - Annual Review of Plant Biology

JF - Annual Review of Plant Biology

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Spatial Features and Functional Implications of Plant 3D Genome Organization

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