Doctor of Philosophy (PhD)
The ribosomal RNA genes of Drosophila melanogaster reside within centromere-proximal nucleolar organizers on both the X and Y chromosomes. Each locus contains between 200-300 tandem repeat rDNA units that encode 18S, 5.8S, and 28S ribosomal RNAs (rRNAs) for ribosome biogenesis. In arthropods like Drosophila, about 60% of rDNA genes are inserted with R1 and/or R2 retrotransposons at specific sites within the 28S regions; these units likely fail to produce functional 28S rRNA. We showed previously that R2 expression increases upon nucleolar stress caused by the loss of a ribosome assembly factor, the Nucleolar Phosphoprotein of 140 kDa (Nopp140). Here we show that R1 expression is selectively induced by heat shock. Actinomycin D, but not α-amanitin, blocked R1 expression in S2 cells upon heat shock, indicating that R1 is transcribed by Pol I. RT-PCR analysis confirmed read-through transcription by Pol I from the 28S gene region into R1. Using a genome wide precision run-on sequencing (PRO-seq) data set available at NCBI-GEO, we showed that Pol I activity on R1 elements is negligible under the normal non-heat shock condition but increases dramatically upon heat shock. We propose that prior to heat shock, Pol I pauses within ~350 bp of the 5’ end of R1 wherein we find ‘pause button’ like sequence motifs, and that heat shock releases Pol I for read-through transcription into R1.
Raje, Himanshu Shekhar, "R1 Retrotransposons in Drosophila melanogaster are Transcribed by RNA Polymerase I Upon Heat Shock" (2018). LSU Doctoral Dissertations. 4523.