The role of histone variants in chromatin organization

The mechanisms that determine the organization and function of specific domains within chromatin are still largely unclear. Plants have diversified the number of core histone H2A variants. These variants index the major types of chromatin and our unpublished data has established that each H2A variant combines with a specific set of histone modifications to define distinct chromatin states. Computational analyses suggest that these chromatin states tightly control genomic functions. Here, we propose to investigate the role of H2A variants in organizing chromatin states and regulating their function. To answer this question using Arabidopsis we will first compare standard chromatin states in somatic cells with reproductive cell types, which lack specific H2A variants. We will also study the impact of the loss of specific H2A variants on chromatin states using specific genetic backgrounds in Arabidopsis and a molecular evolutionary strategy based on model species of alga and bryophytes. This project will establish how and to what degree H2A variants organize chromatin into functional domains of the genome. 1

A key step in evolution of our ancestors from pre-existing bacteria and archaebacteria was the multiplication of histones that control the expression and preservation of the genome. How histone variation impacts the way our cells interpret and use their genome is the focus of the research of the Berger lab. In this proposal we defined that histone variants are pivotal in the distinction of territories occupied by genes and transposable elements of foreign origin. We showed that originally the distinction of foreign genetic material was mediated by the specific histone methylation H3K27me3. This is still the case in many diverse forms of unicellular organisms such as algae and diatoms. During evolution new forms of histone variants were innovated to distinguish the foreign genetic material. These supplanted the original usage of H3K27me3 which became repurposed to silenced genes in animals and plants. We demonstrated that in flowering plants the histone variants organize distinct specific environments around the DNA that flag genes to be used for production of proteins from genes to be kept silent at a particular time of development or in response to various forms of stress. Using algae and plants related to mosses we discovered how the increasing complexity of histone variants evolved in plants to increase the complexity of the regulatory environment of genes. In conclusion, results of this proposal shine a new light on the importance of histone variants in the evolution of the regulations of the genome that were instrumental in the development of complex plants and animals where histone variants are central in the regulation of genomic activities.