# Characterization of the role of biomolecular condensates in gene regulation by small RNAs

> **NIH NIH F31** · JOHNS HOPKINS UNIVERSITY · 2020 · $39,120

## Abstract

Project Summary:
 The near-universal conservation of small RNAs (sRNAs) as a way of regulating gene expression and
the demonstrated importance of this for germline maintenance underscores the need for understanding the
mechanisms by which these agents control their mRNA targets. Prior work studying the localization of proteins
required for this process in different developmental models has shown that many components of the sRNA
machinery localize to perinuclear structures within the germline, known generally as nuage. In C. elegans,
factors such as Argonaute proteins required for sRNA targeting and RNA-dependent RNA polymerases
(RdRPs) needed for amplifying sRNA signals have been observed to be enriched within these perinuclear
organelles. The significance of these structures and how they facilitate sRNA related processes, however,
remains unknown and has become a topic of intense interest. While the cell biology of sRNA protein factors
has been previously characterized, a well-documented study of how RNAs are localized when targeted by this
process remains to be conducted. In an effort to address this gap in the field, we have for the first time
visualized RNAs in the process of being knocked down by sRNAs in a developmental context. By initiating the
sRNA-mediated knockdown of transcripts though RNAi interference (RNAi), I have found that upon RNAi
treatment, targeted RNAs become specifically enriched within the nuage, which houses the very factors
required for sRNA-mediated silencing, such as RdRPs. This exciting observation now opens the doors into
studying the sRNA pathway through a previously uncharted cell biological lens. I hypothesize that recruitment
of sRNA-targeted RNAs into nuage aids in RdRP-mediated amplification of sRNAs against the transcript. To
study the basis for this newly characterized cell biological phenomenon, I will first explore the molecular
players required for this sRNA-induced RNA recruitment as described in my first aim. Using known RNAi
mutants, I will systematically assess each mutant's ability to accumulate RNAs within nuage on a cell biological
level upon induction with RNAi. Furthermore, I will complement this analysis with an unbiased RNA-centric
proteomics approach to identify factors that may be responsible for this RNAi-induced recruitment. In my
second aim, I will assay the effects that concentrating RNAs within condensates could have on RdRP activity
through an in vitro analysis of condensate residency on RdRP kinetics. Altogether, this proposal seeks to
understand a newly identified aspect of sRNA targeting that could have profound implications in human health
and fertility given the conservation of nuage and small RNA pathways in the human germline.

## Key facts

- **NIH application ID:** 10068434
- **Project number:** 1F31HD103428-01
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** John Paul Tsu Ouyang
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $39,120
- **Award type:** 1
- **Project period:** 2020-09-01 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10068434

## Citation

> US National Institutes of Health, RePORTER application 10068434, Characterization of the role of biomolecular condensates in gene regulation by small RNAs (1F31HD103428-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10068434. Licensed CC0.

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