Maintenance and dynamic reprogramming of chromatin organization during development

Abstract

SUMMARYControlled transcription of genes is critical for cell differentiation and development. Gene expression regulation therefore involves a multilayered control from nucleosome composition in histone variants and their post‐translational modifications to higher‐order folding of chromatin fibers and chromatin interactions in nuclear space. Recent technological advances have allowed gaining insight into these mechanisms, the interplay between local and higher‐order chromatin organization, and the dynamic changes that occur during stress response and developmental transitions. In this review, we will discuss chromatin organization from the nucleosome to its three‐dimensional structure in the nucleus, and consider how these different layers of organization are maintained during the cell cycle or rapidly reprogrammed during development.

Transcriptional reactivation of the tRNASer/tRNATyrgene cluster inArabidopsis thalianaroot tip

“…Developmental transitions have been pivotal in the understanding of CH dynamics (Benoit et al, 2013; Simon and Probst, 2023). Particularly, germination associates with a decompaction of CH which promotes the expression of the silent fraction of 5S rDNA clusters in A. thaliana cotyledons (Mathieu et al, 2003).…”

“…Alleviating DNA methylation has no impacts on the silencing of tRNA Pro gene clusters (Hummel et al, 2020). While DNA methylation profile at the SYY cluster doesn’t change along root, the compaction of nucleosomes as their composition in histone variants might be more dynamic parameters during development (Rosa et al, 2014; Zhang et al, 2021; Probst et al, 2020; Probst, 2022; Feng et al, 2022; Simon and Probst, 2023). Around 150bps, the size of tRNA genes is subnucleosomal.…”

Involvement of the H3.3 Histone Variant in the Epigenetic Regulation of Gene Expression in the Nervous System, in Both Physiological and Pathological Conditions

“…The chromatin structure is highly dynamic and changes in different cells during development and differentiation; it also changes in terminally differentiated cells in response to specific inducing factors, such as, for example, thyroid or steroid hormones [11]. At least three connected mechanisms are known to induce structural rearrangements of chromatin (Figure 1): (i) post-translational modification (PTM) of histone proteins [10,12] together with DNA methylation [10,13,14]; (ii) the activity of ATP-dependent complexes that are able to induce modifications in the structure/position of nucleosomes [15], and, finally, (iii) the synthesis and incorporation of histone variants into chromatin [7,[16][17][18]. Herein, we will mainly focus on the latter mechanism (Figure 1, pathway c) and, in particular, on the specific involvement of the H3 histone variant, known as H3.3 core histone, in the epigenetic regulation of gene expression in the nervous system during maturation, as well as in the acquisition of complex functions such as learning and memory.…”

“…The chromatin structure is highly dynamic and changes in different cells during development and differentiation; it also changes in terminally differentiated cells in response to specific inducing factors, such as, for example, thyroid or steroid hormones [ 11 ]. At least three connected mechanisms are known to induce structural rearrangements of chromatin ( Figure 1 ): (i) post-translational modification (PTM) of histone proteins [ 10 , 12 ] together with DNA methylation [ 10 , 13 , 14 ]; (ii) the activity of ATP-dependent complexes that are able to induce modifications in the structure/position of nucleosomes [ 15 ], and, finally, (iii) the synthesis and incorporation of histone variants into chromatin [ 7 , 16 , 17 , 18 ].…”

Advances in plant chromatin

“…Lauriane Simon and Aline V. Probst offer a comprehensive view of epigenetic chromatin changes. They discuss the consequences of these changes for reprogramming gene activity and the 3D chromatin structure in the nucleus, from the nucleosomal level to chromosomal territories (Simon & Probst, 2024). They also address important and still partially enigmatic issues of the maintenance of chromatin states through DNA replication and reprogramming of the epigenome in certain developmental phase transitions.…”