Repression of interrupted and intact rDNA by the SUMO pathway in Drosophila melanogaster

Abstract

Ribosomal RNAs (rRNAs) are essential components of the ribosome and are among the most abundant macromolecules in the cell. To ensure high rRNA level, eukaryotic genomes contain dozens to hundreds of rDNA genes, however, only a fraction of the rRNA genes seems to be active, while others are transcriptionally silent. We found that individual rDNA genes have high level of cell-to-cell heterogeneity in their expression in Drosophila melanogaster. Insertion of heterologous sequences into rDNA leads to repression associated with reduced expression in individual cells and decreased number of cells expressing rDNA with insertions. We found that SUMO (Small Ubiquitin-like Modifier) and SUMO ligase Ubc9 are required for efficient repression of interrupted rDNA units and variable expression of intact rDNA. Disruption of the SUMO pathway abolishes discrimination of interrupted and intact rDNAs and removes cell-to-cell heterogeneity leading to uniformly high expression of individual rDNA in single cells. Our results suggest that the SUMO pathway is responsible for both repression of interrupted units and control of intact rDNA expression.

Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon

“…At the same time, the loss of piRNA-binding protein Piwi on a specific genetic background may cause general transcriptional repression of the rDNA cluster, which leads to partial removal of Udd from the nucleoli of nurse cells ( 107 ). In parallel with our investigations, it was shown that knockdowns of SUMO (Small Ubiquitin-like Modifier) and SUMO ligase Ubc9 induce dramatic derepression of inserted rDNA units and, probably, activation of silent rDNA repeats lacking R1/R2 insertions ( 108 ). The authors suggest that multiple chromatin proteins associated with silenced rDNA units undergo SUMOylation.…”

A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary

“…R1 or R2 showed no de-repression in ovaries lacking Piwi (even when depleted via the MTD-Gal4 driver) although germline Piwi is loaded with R1 and R2 derived piRNAs. In agreement with a recent report (L uo et al . 2020), our data indicate that the SUMOylation pathway is integral for silencing R1 and R2 , likely in a piRNA-independent and to a large extent also in a Su(var)2-10 independent manner.…”

“…2019; K neuss et al . 2019), and on the protein SUMOylation machinery with the E1 activating enzyme Uba2–Aos1 and the E3 Ligase Su(var)2-10 (N inova et al . 2020).…”

“…Depletion of these general factors via MTD-Gal4 driven transgenic RNAi yields rudimentary ovaries with absent germline tissue. To explore the utility of the TOsk-Gal4 system, we focused on the protein SUMOylation pathway that is involved in numerous chromatin-related processes and that is required for Piwi-mediated transcriptional silencing and heterochromatin formation (G areau and L ima 2010; J entsch and P sakhye 2013; N inova et al . 2020).…”

“…A handful of E3 ligases potentiate the SUMOylation process in a substrate specific manner. Recent work has uncovered a critical role for the E3 ligase Su(var)2-10, and hence SUMOylation, in Piwi-mediated heterochromatin formation (N inova et al . 2020).…”