Chromatin domains in space and their functional implications

Frédéric Pontvianne,Chang Liu

doi:10.1016/j.pbi.2019.11.005

Abstract

Genome organization displays functional compartmentalization. Many factors, including epigenetic modifications, transcription factors, chromatin remodelers, and RNAs, shape chromatin domains and the three-dimensional genome organization. Various types of chromatin domains with distinct epigenetic and spatial features exhibit different transcriptional activities. As part of the efforts to better understand plant functional genomics, over the past a few years, spatial distribution patterns of plant chromatin domains have been brought to light. In this review, we discuss chromatin domains associated with the nuclear periphery and the nucleolus, as well as chromatin domains staying in proximity and showing physical interactions. The functional implication of these domains is discussed, with a particular focus on the transcriptional regulation and replication timing. Finally, from a biophysical point of view, we discuss potential roles of liquid-liquid phase separation in plant nuclei in the genesis and maintenance of spatial chromatin domains.

Highlights

In eukaryotes, the nuclear DNA is wrapped around histone octamers to form the chromatin
Large chromatin regions associate at the nuclear periphery with a network composed of lamin fibers are named Lamina-associated domains (LADs) [4]
Some chromatin domains associate with the nucleolar periphery, which belongs to nucleolus, and are named nucleolus-associated chromatin domains (NADs)

Summary

Introduction

The nuclear DNA is wrapped around histone octamers to form the chromatin. Based on a recent rice ChIA-PET study, coordinated expression of active genes can be found among those connected by chromatin loops [35] Together, these results strongly suggest that active chromatin domains in plant nuclei can form extensive physical contacts via chromatin interactions. The cooperative interactions among multiple transcribed loci form a spatial domain of “transcriptional ecosystem equilibrium” in the nucleus that fosters co-expression patterns [57] Such physical interactions among active chromatin could be a mechanism underlying coexpression of metabolic genes residing close to each other (i.e., members belonging to a gene cluster annotated in the linear genome) [58,59]. Important progress have been made, plant cells specificity makes the use of these techniques more challenging (Dumur et al 2019)

Kouzarides T

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