Background
Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant
Arabidopsis
, 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 of
Arabidopsis
linker histones. We show that H1-deficient plants are 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 on hetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of most transposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatial arrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately the transcription but reveal a subset of H1-sensitive genes.
Conclusions
H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization in
Arabidopsis
with 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 may contribute to the epigenetic control of developmental and cellular transitions.
Electronic supplementary material
The online version of this article (10.1186/s13059-019-1767-3) contains supplementary material, which is available to authorized users.
1Chromatin in eukaryotes provides a tunable platform to control gene expression and convey an 2 epigenetic memory throughout cell divisions. H1 linker histones are abundant components with an 3 intrinsic potential in influencing chromatin structure and function. We detail the impact of H1 depletion 4in Arabidopsis on fine-scale chromatin organization, transcription and development. While required for 5 chromocenter assembly, H1s are dispensable for transposable element (TE) silencing and peripheral 6 positioning of heterochromatin. In euchromatin, H1 regulates nucleosome density, mobility, and regular 7 distribution of nanoscale chromatin domains. While necessary to maintain epigenetic patterns, H1 only 8 moderately affects transcription. Its depletion is associated with failures in transitional fate changes 9 such as lateral root initiation, root hair production, stomata patterning but also flowering and dormancy 10 regulation. Therefore, Arabidopsis H1 variants are chromatin architects mediating nano-and microscale 11 levels-of-organization operating downstream of epigenetic and transcriptional establishment processes 12 and contribute to epigenetic reorientations in developmental transitions. 13
Background: Elucidating the genetic and molecular control of plant reproduction requires the deployment of functional approaches based, for instance, on reverse or forward genetic screens. The loss-of-function of essential genes, however, may lead to plant lethality prior to reproductive developmentt or to the formation of sterile structures before the organ-of-interest can be analysed. In these cases, inducible approaches that enable a spatial and temporal control of the genetic perturbation are extremely valuable. Genetic induction in reproductive organs, such as the ovule, deeply embedded in the flower, is a delicate procedure that requires both optimization and validation. Results: Here we report on a streamlined procedure enabling reliable induction of gene expression in Arabidopsis ovule and anther tissues using the popular pOP/LhGR Dex-inducible system. We demonstrate its efficiency and reliability using fluorescent reporter proteins and histochemical detection of the GUS reporter gene. Conclusion: The pOP/LhGR system allows for a rapid, efficient and reliable induction of transgenes in developing ovules without compromising developmental progression. This approach opens new possibilities for the functional analysis of candidate regulators in sporogenesis and gametogenesis, which are otherwise affected by early lethality of conventional, stable mutants.
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