The histone variant H2A.W: a novel component that structures chromatin domains

DNA is wrapped around nucleosomes that are made of two of each core histones H2A, H2B, H3 and H4. We have identified a new core histone variant H2A.W that occupies the major portion of the condensed heterochromatin in plants. Heterochromatin is a key feature that is essential for genome integrity through repression of transposon and for transmission through cell division because of the link between heterochromatin and the mitotic kinetochores. We showed that H2A.W is largely responsible for organization of heterochromatin into higher order dense chromocenters. Here, we wish to assess the impact of H2A.W on chromatin architecture analyzed and represented by Hi-C approach and confront these data with chromatin structure revealed at high definition by super-resolution microscopy. In addition we have shown that H2A.W participates in transcriptional silencing but we do not know the molecular mechanisms involved. Here, we wish to test whether non-coding RNAs participate in this process using a genome-wide deep sequencing strategy. Altogether the project will enhance our understanding of the organization of the cell nucleus and its role in silencing genome expression. The project is based on collaboration between the Berger Lab at GMI in Vienna which contributes expertise in bench work on histone variants and the Chen Lab at Academia Sinica in Taipei whose members contribute their expertise in bioinformatics.

Mobility of transposons, discovered by Barbara McClintock in the middle of the 20th century, poses a threat to genome integrity. However, most transposons are silenced and enriched in specific regions of the genome called heterochromatin. If this silencing mechanism is lost, transposons can be mobilized, with deleterious consequences, as shown in tumor formation. Maintenance of heterochromatin is relatively well investigated, but how silencing by heterochromatin is mediated in the first place is poorly understood and the main question of the project.The lab of Dr. Frederic Berger, who hosted the proposed work, discovered that heterochromatin predominantly contains a distinct variant of histone H2A, one of the four histone types that constitute the building blocks of chromatin. It is hypothesized that the dynamic deposition of the specific variant, called H2A.W, is responsible for establishing heterochromatin and silencing transposons in plants. The project led in collaboration with Dr. Pao-Yang Chen at Academia Sinica confirmed this hypothesis. Based on a combination of genetics and genomics experiments we showed that H2A.W plays a key role in transposon silencing. Pathways that cause DNA methylation assist H2A.W to this effect. These new findings favor the idea that chromatin structure is directly involved in the control of silencing. The findings will have a wide impact on understanding heterochromatin establishment in a broad range of species including humans and mechanisms of chromatin-related diseases.