# Deciphering the germline-specific mechanisms regulating piRNA gene expression from large genomic domains

> **NIH NIH F31** · YALE UNIVERSITY · 2022 · $46,752

## Abstract

Project Summary/Abstract
The Piwi-interacting RNA (piRNA) pathway is a conserved small RNA pathway that protects germ cells from
consequences arising from active foreign genetic elements such as transposons. In C. elegans, >10,000
sequence-diverse piRNA genes cluster in two distinct megabase-scale regions in the genome. piRNA
clustering is conserved across nematode species, implying that it is important for piRNA expression. Despite
being clustered within distinct genomic regions, piRNA genes are individually transcribed by RNA Polymerase
II (RNA pol II) and the resulting short RNAs are suggested to be produced when RNA pol II is in its “paused”
state. The goal of this proposal is to understand how over 10,000 piRNAs are coordinately upregulated from
these large genomic domains in a germline-specific manner. Our lab and others identified the transcription
factors SNPC-4 and PRDE-1, which form a complex that spreads across piRNA gene clusters specifically in
the germ line to promote piRNA production. However, the mechanism by which SNPC-4/PRDE-1 coordinates
piRNA gene expression is unknown. I hypothesize that SNPC-4/PRDE-1 spreading mediates piRNA
biogenesis by affecting chromatin organization and/or controlling transcriptional activity. Recently, our
lab developed a reliable technique to isolate germ nuclei (IGN) at quantities for large scale genomic assays,
which I will use to define at high resolution and specificity the germline-specific patterns of chromatin
organization and transcriptional machinery of piRNA gene clusters. To date, I have isolated germ nuclei from
wildtype and prde-1 mutants and investigated three candidate histone modifications using ChIP-seq, and
observed a global change in repressive histone modifications. By combining the IGN technique with a variety
of genomic approaches, I aim to investigate whether SNPC-4/PRDE-1 coordinate piRNA expression by
influencing chromatin organization (Aim 1), and transcriptional events (Aim 2). In Aim 1, I will investigate
whether SNPC-4/PRDE-1 affect chromatin accessibility across the piRNA gene clusters and whether the local
chromatin environment affects SNPC-4/PRDE-1 binding. In Aim 2, I will investigate whether SNPC-4/PRDE-1
aids in RNA Pol II recruitment and whether SNPC-4/PRDE-1 interact with factors that control the paused state
of RNA Pol II. In addition, I will determine if the RNA Pol II paused state affects SNPC-4/PRDE-1 binding at
piRNA gene clusters. Completion of these aims will advance our understanding of piRNA biogenesis by
deciphering the mechanisms that control chromatin organization and transcriptional machinery of the piRNA
gene clusters, which is essential for germline maintenance and function. Ultimately, this work is likely to be
relevant to understanding the mechanisms that underlie regulation of complex gene regulatory loci in many
different genomes across species.

## Key facts

- **NIH application ID:** 10387717
- **Project number:** 1F31GM145178-01
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Nancy Paniagua
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $46,752
- **Award type:** 1
- **Project period:** 2022-01-01 → 2023-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10387717

## Citation

> US National Institutes of Health, RePORTER application 10387717, Deciphering the germline-specific mechanisms regulating piRNA gene expression from large genomic domains (1F31GM145178-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10387717. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*