Abstract
Background : Chromatin provides a tunable platform for gene expression control. Besides the well-studied corenucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatinfunction. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages forinstance plants. Notably, in the model plantArabidopsis, while H1 is known to influence heterochromatin and DNA methylation, its contribution to transcription, molecular, and cytological chromatin organization remains elusive.Results : We provide a multi-scale functional study ofArabidopsislinker histones. We show that H1-deficient plantsare viable yet show phenotypes in seed dormancy, flowering time, lateral root, and stomata formation—complemented by either or both of the major variants. H1 depletion also impairs pluripotent callus formation. Fine-scale chromatin analyses combined with transcriptome and nucleosome profiling reveal distinct roles of H1 onhetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of mosttransposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatialarrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately thetranscription but reveal a subset of H1-sensitive genes.Conclusions : H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization inArabidopsiswith distinct roles in euchromatin and heterochromatin and a dual causality on gene expression.Phenotypical analyses further suggest the novel possibility that H1-mediated chromatin organization maycontribute to the epigenetic control of developmental and cellular transitions.