Changes in chromatin structure correlate with transcriptional activity of nucleolar rDNA in polytene chromosomes
Abstract
Ribosomal DNA genes (rDNA) are found in tandem arrays of hundreds of repeated genes, but only a fraction of these genes are actively transcribed. The regulatory mechanism controlling the transition between active and inactive rDNA in higher eukaryotes is vital for cell survival. Here, we show that the nucleolus from Drosophila salivary gland cells contains two levels of chromatin organization reflecting differences in transcriptional activity: Decondensed chromatin is highly occupied with TATA-box-binding protein (TBP), phosphorylated H3S10, and acetylated H3K14, suggesting that rDNA in decondensed nucleolar areas is actively transcribed. Condensed chromatin lacks TBP, phosphorylated H3S10, or acetylated H3K14 and is enriched in the rDNA retrotransposons R1 and R2. The data show that R1 and R2 retrotransposons are not actively transcribed in salivary glands and may lead to the epigenetic silencing of flanking rDNA genes and that the silencing mechanisms of these sequences might be partially independent of heterochromatin formation by methylation of histone H3 at lysine 9 and binding of heterochromatin protein 1.
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R2 elements are present exclusively at the rDNA locus, whereas R1 insertions have also been found in other regions of the genome.
“R2 elements are of particular interest because they are present exclusively at the rDNA locus, whereas R1 insertions have also been found in other regions of the genome (35–38).”
From Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon (2022) · cites this paper as [38]
R1 and R2 elements colocalize with condensed chromatin in the nucleolus of salivary gland cells.
“Nevertheless, another report found the colocalization of R1 and R2 elements with condensed chromatin in the nucleolus of salivary gland cells (38).”
From Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon (2022) · cites this paper as [38]
Cites
Ritossa, F. M., Atwood, K. C., & Spiegelman, S. (1966) · Genetics · doi:10.1093/genetics/54.3.819 · Cited by 296 · see citing works
Zhou, Y., Santoro, R., & Grummt, I. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf460 · Cited by 234 · cited 4× · see citing works
“Heterochromatin protein 1 and dimethylated histone H3 at lysine 9 partially correlate with condensed DAPI-stained nucleolar rDNA In addition to deacetylation of H3, heterochromatin formation in rDNA is also accompanied by deacetylation of histone H4 (Earley et al. 2006; Zhou et al. 2002).”
BackgroundInfluentialNucleolar dominance: a model for rRNA gene silencing
McStay, B. (2006) · Genes & Development · doi:10.1101/gad.1436906 · Cited by 95 · see citing works
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“…it has been estimated that, in certain stocks, approximately 240 rDNA genes may be uninserted and transcriptionally functional and yet, based in bobbed mutations, the total number of active rDNA genes required for normal development and cell function is only around 24 (Ye and Eickbush 2006).”
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Guerrero, P. A., & Maggert, K. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016401 · Cited by 51 · see citing works
Fefelova, E. A., Pleshakova, I. M., Mikhaleva, E. A., Pirogov, S. A., Poltorachenko, V. A., Abramov, Y. A., Romashin, D. D., Shatskikh, A. S., Blokh, R. S., Gvozdev, V. A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1276 · Cited by 15 · see citing works
“Nevertheless, another report found the colocalization of R1 and R2 elements with condensed chromatin in the nucleolus of salivary gland cells (38).”
Background
- Authors
- Plata, M. P., Kang, H. J., Zhang, S., Kuruganti, S., Hsu, S.-J., & Labrador, M.
- Affiliations
- University of Tennessee at Knoxville (US)
- Corresponding author
- Labrador, Mariano
- ORCID
- Labrador, Mariano
- Venue
- Chromosoma
- Published
- 2008-12-09
- Volume
- 118
- Issue
- 3
- Pages
- 303-322
- ISSN
- 0009-5915 (ISSN-L)
- 1432-0886
- OpenAlex
- W2037087353
- Cited by
- 12
- References
- 6
- Citations by year
- 2025: 3 · 2022: 2 · 2021: 1 · 2013: 1
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Chromosoma (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation
- National Institutes of Health
- National Institute of General Medical Sciences (R21GM078132, GM78132-2)
- Topics
- 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
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- ribosomal DNA, nucleolus, chromatin structure, rDNA transcription, polytene chromosomes, Drosophila salivary gland, TATA-binding protein, histone H3K14 acetylation, epigenetic silencing, heterochromatin, histone H3 lysine 9 methylation, HP1, chromatin decondensation
- MeSH terms
- Animals, Cell Nucleolus, Chromatin, Chromosomes, DNA, Ribosomal, Drosophila, Histones, Salivary Glands, Genes, Insect, Retroelements, TATA-Box Binding Protein
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