Characterization of a novel family of nucleolus localized RNAs

Eukaryotic cell nucleus is compartmentalized into various non-membranous sub-nuclear domains with nucleolus being the most prominent one. The nucleolus is the largest sub-nuclear domain where ribosomal gene transcription, pre-rRNA processing, and the initial steps of ribosome sub-unit assembly take place. In human cells, nucleoli are formed around nucleolar organizer regions (NORs) located on the short arms of the five acrocentric chromosomes. NORs are composed of tandem copies of hundreds of rDNA repeats. However, the sequence beyond the rDNA array within the p-arms of NOR containing acrocentric chromosomes is largely unknown. In human cells, ~400 copies of rDNA repeats code for rRNAs. Interestingly, at any time point only ~50% of rRNA genes remain transcriptionally active. While the dynamic changes in histone or DNA modifications on rDNA regulatory elements, and noncoding RNAs have been implicated in regulating the transcription of individual rRNA genes, the precise mechanism of how ~50% of rRNA genes remains silenced at any time point is yet to understand. In Chapter II, I focus on the characterization of a novel abundant family of ncRNAs, Single NUcleolus Localized RNA (SNUL-RNA). SNUL-RNAs decorate individual nucleolus in the form of a ‘cloud’ in primary and transformed human cells. Super-resolution microscopy imaging revealed that SNUL-RNA showed similar nuclear distribution to pre-rRNA. Further studies suggested that SNUL-RNA is transcribed by RNA Pol I and behaves similarly to pre-rRNA during biological processes when the nucleolar structure is disrupted. Long-read RNA-sequencing analyses indicate that full-length SNULs show significant similarities to pre-rRNAs, implying that SNULs could be evolved from duplications of rDNA genes during evolution. Intriguingly, SNUL-RNAs are found to ‘coat’ the p-arm of NOR-containing chromosomes in a monoallelic fashion, and this monoallelic expression of SNUL-RNAs is epigenetically inheritable and potentially regulated by histone and DNA modifications. Loss-of-function studies reveal that SNUL-RNAs might play a negative regulatory role on rRNA biogenesis. My studies emphasized that not all nucleoli within a cell are functionally identical and NORs on different acrocentric chromosomes are distinct from each other. It also revealed a novel RNA-mediated mechanism for regulating rDNA gene expression and nucleolar function.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Cell and Developmental Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2021

Author dc:creator

• Hao, Qinyu

Contributors dc:contributor

• Kannanganattu, Prasanth V
• Prasanth, Supriya G
• Belmont, Andrew S
• Ceman, Stephanie
• Kalsotra, Auinash

• SNUL-1
• long non-coding RNA
• nucleolus
• rRNA biogenesis

Statement dc:rights

• Copyright 2021 Qinyu Hao

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/110832

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/110832