Ribosome biogenesis disruption mediated chromatin structure changes in C. elegans larvae revealed by SRAtac, an integrated, customizable end to end analysis pipeline for ATAC-seq

Nucleolus is the largest nuclear body and the site of ribosome biogenesis. Recent studies implicated an important role for nucleolus as an organizer of chromatin architecture. However, lack of genetic tools to disrupt nucleolar ribosome biogenesis limited our understanding of the causal link between chromatin architecture and nucleolar ribosome assembly. Here, we introduce SRAlign, a reproducible, configurable, and extensible NGS data processing workflow as well as SRAtac, a customizable and end to end analysis pipeline for ATAC-seq analysis. We apply these methods to determine the changes in chromatin accessibility upon specific depletion of an RNA polymerase I subunit, RPOA-2, a ribosome biogenesis components RRB-1 in Caenorhabditis elegans. We found highly comparable changes in chromatin accessibility in response to these two perturbations. However, the identified chromatin accessibility changes are weakly correlated with gene expression changes. Our results support feedback from nucleolar ribosome biogenesis to chromatin structure during the L1 stage in C. elegans but question the significance of these changes on gene expression. Overall design: Comparative chromatin structure studies analysis of ATAC-seq data in Caenorhabditis elegans specifically depleted of nucleolus and translation components RPOA-2 and RRB-1.