How is RNA silencing spatially organized?
A fundamental question in RNA biology is how cells distinguish RNAs that should be expressed from those that should be silenced. Our laboratory approaches this problem by investigating the spatial organization of RNA silencing pathways within germ granules, specialized biomolecular condensates that coordinate multiple steps of small RNA-mediated gene regulation.
Our work has shown that germ granules are organized into distinct, hierarchically assembled compartments that form an ordered network surrounding the nucleus. Rather than serving as passive storage sites, these condensates selectively organize RNA silencing machinery and likely route RNAs through successive stages of recognition and processing. We are now identifying the molecular mechanisms that establish this organization, defining new germ granule components and their interactions, and determining how condensate architecture influences RNA silencing, transgenerational inheritance, and genome stability.
Selected Publications:
Chen, S, Prescott LH, Mello CC, Phillips CM. Systematic Identification of Germ Granule Proteins Reveals Specialized Roles in RNAi and Small RNA Inheritance. bioRxiv. 2026 PDF
Uebel CJ, Rajeev S, Phillips CM. Caenorhabditis elegans germ granules are present in distinct configurations and assemble in a hierarchical manner. Development. 2023 PDF
Manage KI et al. A Tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans. eLife. 2020 PDF
Uebel CJ et al. Distinct regions of the intrinsically disordered protein MUT-16 mediate assembly of a small RNA amplification complex and promote phase separation of Mutator foci. PLoS Genet. 2018 PDF
How do Argonaute proteins achieve specificity?
Small RNAs regulate gene expression by associating with Argonaute proteins, yet many Argonautes recognize highly similar small RNAs while directing distinct biological outcomes. How these proteins achieve remarkable specificity remains one of the central questions in the field.
Our research has uncovered multiple mechanisms that contribute to Argonaute specificity, including intrinsic small RNA preferences, protein-protein interactions, post-translational modifications, developmental regulation, and spatial compartmentalization within germ granules. By combining genetics, genomics, biochemistry, and quantitative imaging, we seek to understand how these mechanisms work together to ensure that each Argonaute engages the correct small RNAs and targets the appropriate transcripts.
Selected Publications:
Chen S, Phillips CM. Nuclear Argonaute protein NRDE-3 switches small RNA partners during embryogenesis to mediate temporal-specific gene regulatory activity. Elife 2025 link
Chen S, Phillips CM. HRDE-2 drives small RNA specificity for the nuclear Argonaute protein HRDE-1. Nat Commun. 2024 PDF
Nguyen DAH, Phillips CM. Arginine methylation promotes siRNA-binding specificity for a spermatogenesis-specific isoform of the Argonaute protein CSR-1. Nat Commun. 2021 PDF
How do post-translational modifications regulate RNA silencing?
RNA silencing pathways must be dynamic, allowing cells to rapidly adjust gene regulation in response to developmental and environmental cues. We study how post-translational modifications—including arginine methylation, phosphorylation, and ubiquitination—control the activity, localization, stability, and interactions of Argonaute proteins and other RNA silencing factors.
Our work has demonstrated that arginine methylation regulates small RNA specificity and links primary and secondary RNA silencing pathways. We are now investigating how RG motifs and their associated modifications coordinate protein interactions, transgenerational inheritance, and genome stability. In parallel, we are identifying additional post-translational mechanisms that regulate Argonaute turnover and activity, with the goal of understanding how RNA silencing pathways are dynamically controlled in vivo.
Selected Publications:
Zhao, JM, Nguyen DH, Cervantes D, Vong B, Phillips CM. The Ubiquitin-Proteasome Pathway Mediates Selective Degradation of Unloaded Argonautes in C. elegans. Genetics. 2026 PDF
Wallis DC, Phillips CM. RG motifs promote piRNA-mediated gene silencing in C. elegans. Nucleic Acids Res. 2025 PDF
Nguyen DAH, Phillips CM. Arginine methylation promotes siRNA-binding specificity for a spermatogenesis-specific isoform of the Argonaute protein CSR-1. Nat Commun. 2021 PDF