Linking transcriptional silencing with chromatin remodeling, folding, and positioning in the nucleus

Abstract

Chromatin organization is important for many DNA-templated processes in eukaryotic cells such as replication and transcription. Recent studies have uncovered the capacity of epigenetic modifications, phase separation, and nuclear architecture and spatial positioning to regulate chromatin organization in both plants and animals. Here, we provide an overview of the recent progress made in understanding how chromatin is organized within the nucleus at both the local and global levels with respect to the regulation of transcriptional silencing in plants. To be concise while covering important mechanisms across a range of scales, we focus on how epigenetic modifications and chromatin remodelers alter local chromatin structure, how liquid-liquid phase separation physically separates broader chromatin domains into distinct droplets, and how nuclear positioning affects global chromatin organization.

Keywords: Chromatin organization; Epigenetic modifications; Transcriptional regulation.

Figure 1.. Chromatin remodelers function in chromatin organization and transcriptional regulation.

(A) The SWI/SNF2 chromatin remodeling protein DDM1 binds H2A.W and changes the properties of chromatin to allow DNA methyltransferases to access histone H1 containing regions. (B) The CLSY family of chromatin remodelers associates with the H3K9me2 reader protein SHH1 and enables Pol IV recruitment. (C) DRD1 interacts with DMS3 and RDM1 to change nucleosome positioning and facilitate the association of Pol V with chromatin. (D) SWI3B, a subunit of the SWI/SNF chromatin remodeling complex, functions with the Pol V transcript-binding protein IDN2 to establish nucleosome positioning and mediate de novo DNA methylation and transcriptional silencing. MORC family proteins interact with SWI3D and the DNA methylation binding proteins SUVH2/9 to mediate heterochromatin condensation and gene silencing. (E) Chromatin remodelers function in PRC-enriched facultative heterochromatin regulation. Important abbreviations: DDM1, Deceased in DNA Methylation 1; CLSY, SNF2 domain-containing protein CLASSY; SHH1, SAWADEE Homeodomain Homolog 1; Pol IV, DNA-dependent RNA polymerase IV; DRD1, Defective in RNA-Directed DNA methylation 1; DMS3, Defective in Meristem Silencing 3; RDM1, RNA-Directed DNA Methylation 1; Pol V, DNA-dependent RNA polymerase V; IDN2, Involved in De Novo 2; MORC, Microrchidia; SUVH2/9, SU(VAR)3-9 homolog protein 2 and SU(VAR)3-9 homolog protein 9; Pol II, DNA-dependent RNA polymerase II. CHR11/17, imitation of switch (ISWI)-like chromatin-remodeling protein 11 and 17; PIE, Photoperiod-Independent Early flowering; INO80, INOsitol requiring 80; PRC complex, Polycomb Repressive Complex; CLF, Curly LeaF; PKL, PicKLe, CHD3-type chromatin remodeling protein; BRM, BRahMa, SWI/SNF chromatin remodeling protein.

Figure 2.. Phase separation and chromatin condensation at the nuclear periphery.

(A) In the nucleus, chromatin is highly organized into different chromosome territories. Heterochromatin within gene-poor regions is typically found at the nuclear periphery, whereas gene-rich euchromatin is in the nuclear interior. (B) ADCP/AGDP binds H3K9me2, which is established by a self-reinforcing loop between DNA methyltransferases (DRM2 and CMT2/3) and H3K9 methyltransferases (SUVHs), and mediates heterochromatin phase separation and chromocenter formation. Histone linker H1 is proposed to condense heterochromatin and regulate nucleosome position. Histone variants (e.g., H2A.W and H2B.8) are also involved in promoting the formation of nuclear condensates. (C) Plant lamin-like proteins CRWN1/4 and PWO1 function together to link inaccessible chromatin domains and the nuclear matrix. PNET2 is a nuclear membrane protein associated with CRWN1 and KAKU4, and drives heterochromatin to the nuclear periphery. Phase-separated assemblies of proteins and nucleic acids are termed nuclear bodies (e.g., AGO4 body and PcG body). AGO4 bodies colocalize with Pol V subunits and Cajal bodies to establish DNA methylation. PcG bodies are condensates of Polycomb-group (PcG) proteins, which control H3K27me3. Important abbreviations: Pol V, DNA-dependent RNA polymerase V; AGO4, Argonaut 4; CRWN1/4, CROWDED NUCLEI 1 and CROWDED NUCLEI 4; PWO1, PROLINE-TRYPTOPHAN-TRYPTOPHAN-PROLINE INTERACTOR OF POLYCOMBS1; PNET2, Plant Nuclear Envelope Transmembrane 2; DRM2, Domains Rearranged Methyltransferase 2; CMT2/3, CHROMOMETHYLASE 2 and CHROMOMETHYLASE 3; SUVHs, SU(VAR)3-9 HOMOLOG proteins; ADCP/AGDP, Agenet Domain Containing Protein 1/Agenet Domain (AGD)-Containing P1.