You shall not pass! A Chromatin barrier story in plants

Abstract

As in other eukaryotes, the plant genome is functionally organized in two mutually exclusive chromatin fractions, a gene-rich and transcriptionally active euchromatin, and a gene-poor, repeat-rich, and transcriptionally silent heterochromatin. In Drosophila and humans, the molecular mechanisms by which euchromatin is preserved from heterochromatin spreading have been extensively studied, leading to the identification of insulator DNA elements and associated chromatin factors (insulator proteins), which form boundaries between chromatin domains with antagonistic features. In contrast, the identity of factors assuring such a barrier function remains largely elusive in plants. Nevertheless, several genomic elements and associated protein factors have recently been shown to regulate the spreading of chromatin marks across their natural boundaries in plants. In this minireview, we focus on recent findings that describe the spreading of chromatin and propose avenues to improve the understanding of how plant chromatin architecture and transitions between different chromatin domains are defined.

PlantFUNCO: Integrative Functional Genomics Database Reveals Clues into Duplicates Divergence Evolution

“…For example, RNA polymerase II (Pol2) was significantly located in all active and several bivalent states, and there was enrichment of the well-known H3K9-demethylase (IBM1) and transposon-methylase (CMT3) over heterochromatic states in A. thaliana . Most of the transcription factors (TFs) observed in heterochromatin states were related to flowering, an organ missed in our collection, and cell cycle/division functions, which have been previously described as present in chromatin barriers and strictly under control, with low expression levels ( Feng and Michaels 2015 ; Velay et al 2022 ). Essentially, all noncommon active and repressive histone marks/variants evaluated were enriched in active/bivalent and heterochromatic states, respectively, with only two exceptions: H3K27me1 located in Bivalent Promoter CS2 in A. thaliana , which did not impact the state definition because this was already presented as bivalent due to the presence of H3K27me3; and H3K9me1/me3 in Active gradual bivalent flank > intergenic CS7 in O. sativa .…”

Epigenetic variation in early and late flowering plants of the rubber-producing Russian dandelion Taraxacum koksaghyz provides insights into the regulation of flowering time

“…Most elements in genes were class II transposons 82 , 83 , but Copia-type elements were also found in genes 84 , 85 . This may also be related to the clear boundaries of CHH methylation in the TSS and TES of Helitron, TIR-like and (to a lesser extent) Copia-type elements, which may reflect a balance between active demethylation and de novo methylation by RdDM to prevent heterochromatin spreading into genic regions in A. thaliana 86 , 87 .…”