Monoallelically-expressed Noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression
- University of Illinois Urbana-Champaign, United States
- Indiana University - Purdue University Indianapolis, United States
- National University of Ireland, Galway, Ireland
- Pacific Biosciences, United States
- University of Connecticut Health Center, United States
- Ionis Pharmaceuticals, United States
- Northwestern University, United States
Abstract
Out of the several hundred copies of rRNA genes arranged in the nucleolar organizing regions (NOR) of the five human acrocentric chromosomes, ~50% remain transcriptionally inactive. NOR-associated sequences and epigenetic modifications contribute to the differential expression of rRNAs. However, the mechanism(s) controlling the dosage of active versus inactive rRNA genes within each NOR in mammals is yet to be determined. We have discovered a family of ncRNAs, SNULs (Single NUcleolus Localized RNA), which form constrained sub-nucleolar territories on individual NORs and influence rRNA expression. Individual members of the SNULs monoallelically associate with specific NOR-containing chromosomes. SNULs share sequence similarity to pre-rRNA and localize in the sub-nucleolar compartment with pre-rRNA. Finally, SNULs control rRNA expression by influencing pre-rRNA sorting to the DFC compartment and pre-rRNA processing. Our study discovered a novel class of ncRNAs influencing rRNA expression by forming constrained nucleolar territories on individual NORs.
Data availability
Sequencing data have been deposited in NCBI SRA data base under accession code PRJNA814414
Article and author information
Author details
Swapna Vidhur Daulatabad
Rajneesh Srivastava
Kannanganattu V Prasanth
Funding
National Institute of General Medical Sciences (GM132458)
- Kannanganattu V Prasanth
National Science Foundation (2225264)
- Supriya Prasanth
National Science Foundation (1940422)
- Sarath C Janga
National Science Foundation (1908992)
- Sarath C Janga
National Institute of General Medical Sciences (GM120552)
- Hong Jin
National Institute on Aging (AG065748)
- Kannanganattu V Prasanth
National Institute of General Medical Sciences (GM125196)
- Supriya Prasanth
National Institute of General Medical Sciences (R35GM131819)
- Saurabh Sinha
National Institute on Aging (R21AG065748)
- Sarath C Janga
National Institute of General Medical Sciences (R01GM123314)
- Sarath C Janga
National Science Foundation (1723008)
- Kannanganattu V Prasanth
National Science Foundation (1243372)
- Supriya Prasanth
National Science Foundation (1818286)
- Supriya Prasanth
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Jeannie T Lee, Massachusetts General Hospital, United States
Version history
- Received: May 31, 2022
- Preprint posted: July 4, 2022 (view preprint)
- Accepted: January 18, 2024
- Accepted Manuscript published: January 19, 2024 (version 1)
- Version of Record published: February 8, 2024 (version 2)
Copyright
© 2024, Hao et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Monoallelically-expressed Noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression
eLife 13:e80684.
https://doi.org/10.7554/eLife.80684
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