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EMBO J. 2015 Nov 12;34(22):2758-74. doi: 10.15252/embj.201591458. Epub 2015 Oct 13.

Alu element-containing RNAs maintain nucleolar structure and function.

Author information

1
Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany m.caudron@dkfz.de karsten.rippe@dkfz.de.
2
Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany.
3
Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany.
4
Department of Biochemistry III, Biochemistry Center Regensburg University of Regensburg, Regensburg, Germany.

Abstract

Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.

KEYWORDS:

Alu repeat‐containing RNA; RNA‐dependent phase separation; nucleolus structure and function

PMID:
26464461
PMCID:
PMC4682651
DOI:
10.15252/embj.201591458
[Indexed for MEDLINE]
Free PMC Article

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