# Regulation of gene expression and genome organization by small RNAs

> **NIH NIH R35** · UNIVERSITY OF SOUTHERN CALIFORNIA · 2021 · $441,375

## Abstract

RNA silencing is a gene regulatory mechanism by which small RNAs (18-30 nucleotides) and their Argonaute
protein co-factors modulate the expression of both foreign and endogenous mRNAs. Small RNAs play a critical
role in maintaining proper gene expression by identifying fully or partially complementary mRNAs and targeting
them for either transcriptional or post-transcriptional regulation. The role of RNA silencing in gene regulatory
pathways is conserved across most eukaryotes and is thus of fundamental importance to the developmental and
cellular biology of humans. C. elegans is an excellent system to study RNA silencing because of its short
generation time, its transparency which is ideal for microscopy, and the powerful genetic tools available for
genome manipulation. In C. elegans germ cells, proteins involved in RNA silencing are organized into sub-
compartments of perinuclear condensates, with each sub-compartment playing a unique and critical role. Many
protein factors have been identified that localize to these structures, yet we know little about how they are
organized and assembled. In the first part of this proposal, we will identify factors and conditions that promote
assembly of RNA silencing components into perinuclear condensates. We will further identify the RNAs in each
sub-compartment, with the ultimate goal of dissecting the trajectory of a targeted mRNA through each of its
phases: beginning with transcription, continuing through this assemblage of perinuclear condensates, and
ultimately with translational repression or degradation by the RNA silencing pathway. Because there are ~27 C.
elegans Argonaute proteins, many of which colocalize at P granules, we will next identify the factors contributing
to sorting of small RNA into the appropriate Argonaute proteins. This sorting is critical because many Argonaute
proteins bind different small RNAs from one another, target distinct groups of mRNAs, and can have very
different regulatory effects on these target mRNAs. Finally, we will focus on how protein modifications such as
phosphorylation and methylation can regulate RNA silencing pathways, including affecting localization,
interacting partners, and dynamics of Argonaute proteins and other key factors. Together, the proposed
experiments will uncover the key details of how RNA silencing pathways are organized, how the specificity of
the pathways is defined, and what mechanisms regulate these pathways. This work will lead to a better
understanding of how small RNAs modulate gene expression in healthy cells, which can ultimately be applied to
discerning how changes in these pathways cause misregulation of genes in humans and transition to a disease
state.

## Key facts

- **NIH application ID:** 10202138
- **Project number:** 2R35GM119656-06
- **Recipient organization:** UNIVERSITY OF SOUTHERN CALIFORNIA
- **Principal Investigator:** Carolyn Marie Phillips
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $441,375
- **Award type:** 2
- **Project period:** 2016-09-01 → 2026-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10202138

## Citation

> US National Institutes of Health, RePORTER application 10202138, Regulation of gene expression and genome organization by small RNAs (2R35GM119656-06). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10202138. Licensed CC0.

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