Interplay Between Nucleolus and Chromatin

DOES THE NUCLEOLUS, THE NUCLEUS'S CENTRAL HUB, ACTIVELY CONTRIBUTE TO ORGANIZING GENETIC MATERIAL?

Elucidating Epigenetic Roles of rDNA locus and nucleolus: Multi-copy rDNA locus is the primary determinant of nucleolus formation and mis-regulation of its copy number is associated with enlarged and irregular nucleoli which is a hallmark of malignant cancer. rDNA copy loss is associated with epigenetic mis-regulation, increased DNA damage and massive gene expression changes and is frequently observed in cancer. In Drosophila, induced variation in rDNA copy number modifies heterochromatin-induced silencing and causes expression changes in hundreds to thousands of genes in an isogenic background. Several cancers including osteosarcoma, lymphoma, esophageal adenocarcinoma, lung adenocarcinoma & squamous cell carcinoma and kidney renal clear cell carcinoma were all observed to have reduced rDNA copies which is surprisingly associated with enlarged & irregular nucleoli. Thus, malformation of nucleolus and rDNA-chromatin interactions affect gene expression and essential biological processes beyond ribosome biogenesis.

Nucleolus anchors specific and yet diverse chromatin domains which are called nucleolar associated DNA domains (NADs), as illustrated below. Yet, we lack an understanding whether these NAD regions are specifically tethered and their role in controlling gene expression.

Thus, systematic approaches to elucidate the functions of nucleolus-chromatin interactions is fundamentally important to understand the ribosome biogenesis independent roles of nucleolus in chromatin regulation and gene expression

We've built a user-friendly analysis tool, SRAtac, an end-to-end customizable analysis pipeline for alignment and ATAC-seq analysis across different model organisms. You can find the SRAtac tool, at the following GitHub repositories: https://github.com/trev-f/SRAlign, https://github.com/trev-f/SRAtac

We used SRAtac to investigate the effects of nucleolar modifications on chromatin accessibility. Interestingly, when we disrupt ribosome and ribosomal RNA production, processes that have a direct influence on the nucleolus, we noted analogous chromatin accessibility changees in the non-reproductive (somatic) cells of the organism. These alterations closely parallel the deposition of H3K4 methyl marks observed in response to UV radiation.

Additionally, we have generated the first complete deletion of the ribosomal DNA locus in a metazoan, C. elegans, is the seeder of nucleolus structure. This is valuable for investigating epigenetic function of nucleolus in a multi-cellular organism. Ribosomal DNA locus deleted embryos complete embryogenesis based on maternal ribosomes yet they lack a distinct nucleoli structure, thus enabling a valuable tool to investigate nucleolar function in a multi-cellular organism.