Cited by 13Chromosomal and Genetic VariationsGenomics and Chromatin DynamicsNuclear Structure and Function

R1 retrotransposons in the nucleolar organizers of Drosophila melanogaster are transcribed by RNA polymerase I upon heat shock

Open access
Raje, Himanshu S., Lieux, Molly E., DiMario, Patrick J.·2018·Transcription

Abstract

The ribosomal RNA genes (rDNA) 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, 2S, and 28S ribosomal RNAs (rRNAs) necessary for ribosome biogenesis. In arthropods like Drosophila, about 60% of the rDNA genes have R1 and/or R2 retrotransposons inserted at specific sites within their 28S regions; these units likely fail to produce functional 28S rRNA. We showed earlier that R2 expression increases upon nucleolar stress caused by the loss of the ribosome assembly factor, 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 elements are transcribed by Pol I. A series of RT-PCRs established read-through transcription by Pol I from the 28S gene region into R1. Sequencing the RT-PCR products confirmed the 28S-R1 RNA junction and the expression of R1 elements within nucleolar rDNA rather than R1 elements known to reside in centromeric heterochromatin. Using a genome-wide precision run-on sequencing (PRO-seq) data set available at NCBI-GEO, we show that Pol I activity on R1 elements is negligible under normal non-heat shock conditions but increases upon heat shock. We propose that prior to heat shock Pol I pauses within the 5' end of R1 where we find a consensus "pause button", and that heat shock releases Pol I for read-through transcription farther into R1.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1080/21541264.2018.1506682

Cites

50 of 50 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Raje, H. S., Lieux, M. E., & DiMario, P. J.
Affiliations
Louisiana State University (US)
Corresponding author
DiMario, Patrick J.
Venue
Transcription
Published
2018-08-21
Volume
9
Issue
5
Pages
273-285
ISSN
  • 2154-1264 (ISSN-L)
  • 2154-1272
OpenAlex
W2886167526
Cited by
13
References
50
Citations by year
2025: 6 · 2024: 1 · 2022: 3 · 2021: 1 · 2020: 1 · 2018: 1
FWCI
0.66
Type
journal article
Language
en
Open access
Locations
  • Transcription (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • Civil War Book Review (submittedVersion)
Funders
  • Directorate for Biological Sciences (MCB1712975)
  • U.S. National Science Foundation (MCB1712975)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords
R2 retrotransposon, ribosomal DNA, nucleolar organizer regions, heat shock, RNA polymerase I, read-through transcription, 28S rRNA, Nopp140, nucleolar stress, ribosome biogenesis, Drosophila melanogaster, transcriptional pause
MeSH terms
Animals, Dactinomycin, DNA, Ribosomal, Drosophila melanogaster, Hydrogen Peroxide, Larva, Nucleolus Organizer Region, RNA Polymerase I, RNA, Ribosomal, 28S, Transcription, Genetic, Oxidative Stress, Retroelements, Heat-Shock Response, Nucleic Acid Synthesis Inhibitors

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review