Chromatin domains in space and their functional implications

Abstract

Genome organization exhibits functional compartmentalization. Several 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.

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

“…Eukaryotic chromatin is hierarchically packaged in chromatin loops, TADs, A/B compartments, and CTs ( Figure 1) (well reviewed by Grob and Grossniklaus, 2017;Szalaj and Plewczynski, 2018;Stam et al, 2019;Zheng and Xie, 2019;Pontvianne and Liu, 2020). The principles of 3D genome organization at different scales ranging from chromatin loops to chromosome territories are conserved but distinct between mammals and plants (Do gan and .…”

Nucleolus-associated chromatin domains are maintained under heat stress, despite nucleolar reorganization in Arabidopsis thaliana

“…Fibrillarin proteins indeed possess a strong intrinsically disordered region (IDR) required for the formation of the DFC, that behaves like a phase-separated body (Feric et al 2016). The A. thaliana FIBRILLARIN 2 protein also contains an important IDR (Pontvianne and Liu 2019). These typical ring-like shapes of the DFC are also absent from the nuc1 mutant, where the nucleolus structure is affected and where GC and DFC are hardly detectable (Pontvianne et al 2007).…”

“…For example, in mammalian cells, some proteins are sequestered in the nucleolus during stress conditions (Audas and Lee 2016). The nucleolus also plays an important role in genome organization, by anchoring genomic regions with heterochromatic features at the nucleolar periphery (Nemeth and Langst 2011;Pontvianne and Liu 2019). In a previous study, we identified the nucleolus-associated chromatin domains (NADs) in A. thaliana (Pontvianne et al 2016b).…”

Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

“…The nucleolus plays an important role in the spatial organization of the chromosomes (Bersaglieri and Santoro 2019;Pontvianne and Liu 2020;Santos et al 2020). Nucleolus-associated chromatin domains (NADs), essentially composed of repressed chromatin domains, localize at the nucleolar periphery (Németh et al 2010;van Koningsbruggen et al 2010;Pontvianne et al 2016b).…”