# Structural and Mechanistic basis for RNA Silencing

> **NIH NIH R35** · SCRIPPS RESEARCH INSTITUTE, THE · 2023 · $681,013

## Abstract

Project Summary/Abstract
RNA Silencing is a blanket term for a diverse group of biological processes in which small RNAs, including
PIWI-interacting RNAs (piRNAs), microRNAs (miRNAs), and small interfering RNAs (siRNAs) silence
genes. This proposal aims to leverage my group’s expertise in structural biology and biochemistry to
address outstanding questions that stand as roadblocks to advancing the current understanding of RNA
Silencing biology. Specifically: 1) piRNAs, essential for defending the genome against transposable
elements (TEs), have been studied extensively using molecular genetics, but how piRNA-associated
factors work together to produce the potent TE-silencing observed in animals remains unclear. We will
address this knowledge gap by discovering the structures and biochemical activities of RNA-protein
complexes central to piRNA function. 2) miRNAs are ubiquitous regulators of cellular gene expression in
mammals, but how miRNAs themselves are regulated has only recently come to light. We will advance
this emerging area by determining the structural basis for targeted ubiquitination and destruction of miRNA-
protein complexes by the recently discovered ZSWIM8 Cullin-RING E3 ubiquitin ligase. 3) Although the
canonical function of miRNAs is to silence targeted mRNAs, certain RNA viruses have evolved
mechanisms to repurpose cellular miRNAs to instead stabilize their viral genomes and stimulate viral
production. The mechanisms by which miRNA complexes are redirected to achieve these non-canonical
functions are poorly understood. We are addressing this knowledge gap by investigating interactions
between Hepatitis C Virus (HCV) and the liver-specific miRNA miR-122, with a focus on understanding the
structures of miR-122–HCV RNA complexes that modulate HCV translation to enable replication of HCV
RNA. 4) One of the oldest and most intriguing mysteries of the RNA Silencing field is that, in some cases,
silencing RNAs readily pass between animal cells. 25 years after this discovery, the mechanisms for RNA
transport into animal cells remain unclear. We are addressing this shortcoming by determining the
structural basis for RNA recognition and transport by SID-1, a broadly conserved integral membrane
protein that transports double-stranded RNA into animal cells. The combined studies are expected to
produce insights necessary to overcome the major knowledge barriers described above, with implications
for understanding human health, fertility, viral infection, and the advancement of RNA-based therapies.

## Key facts

- **NIH application ID:** 10623935
- **Project number:** 2R35GM127090-06
- **Recipient organization:** SCRIPPS RESEARCH INSTITUTE, THE
- **Principal Investigator:** IAN JOHN MACRAE
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $681,013
- **Award type:** 2
- **Project period:** 2018-08-01 → 2028-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10623935

## Citation

> US National Institutes of Health, RePORTER application 10623935, Structural and Mechanistic basis for RNA Silencing (2R35GM127090-06). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10623935. Licensed CC0.

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