GH1-HMGA proteins restrict RNA-directed DNA methylation and antagonize linker histone H1 at euchromatic transposable elements

In plant genomes, transposable elements (TEs) are silenced by CG and non-CG DNA methylation, with non-CG methylation maintained by CMT chromomethylases and the RNA-directed DNA methylation (RdDM) pathway. In Arabidopsis, linker histone H1 differentially influences these pathways, as loss of H1 causes non-CG hypermethylation at pericentromeric TEs but hypomethylation at euchromatic TEs in gene-rich regions. The molecular basis of this antagonism has remained unclear. Here, we show that GH1-HMGAs, a family of H1-related High Mobility Group proteins, bind AT-rich sequences at euchromatic TEs and prevent RdDM-dependent non-CG methylation by limiting siRNA accumulation. Furthermore, GH1-HMGA and H1 compete for chromatin association at these TEs, as loss of GH1-HMGA triggers ectopic H1 redistribution, while loss of H1 increases GH1-HMGA enrichment, providing a mechanistic explanation for the non-CG hypomethylation observed in h1 mutants. Collectively, these findings reveal how GH1-HMGA proteins specifically restrain RdDM activity at euchromatic TEs and elucidate how the H1/GH1-HMGA balance spatially partitions distinct DNA methylation pathways across the genome.