Celja Uebel

All Publications

• <i>Caenorhabditis</i><i> elegans</i> germ granules are present in distinct and assemble in a hierarchical manner DEVELOPMENT Uebel, C. J., Rajeev, S., Phillips, C. M. 2023; 150 (24)

  Abstract

  RNA silencing pathways are complex, highly conserved, and perform crucial regulatory roles. In Caenorhabditis elegans germlines, RNA surveillance occurs through a series of perinuclear germ granule compartments - P granules, Z granules, SIMR foci, and Mutator foci - multiple of which form via phase separation. Although the functions of individual germ granule proteins have been extensively studied, the relationships between germ granule compartments (collectively, 'nuage') are less understood. We find that key germ granule proteins assemble into separate but adjacent condensates, and that boundaries between germ granule compartments re-establish after perturbation. We discover a toroidal P granule morphology, which encircles the other germ granule compartments in a consistent exterior-to-interior spatial organization, providing broad implications for the trajectory of an RNA as it exits the nucleus. Moreover, we quantify the stoichiometric relationships between germ granule compartments and RNA to reveal discrete populations of nuage that assemble in a hierarchical manner and differentially associate with RNAi-targeted transcripts, possibly suggesting functional differences between nuage configurations. Our work creates a more accurate model of C. elegans nuage and informs the conceptualization of RNA silencing through the germ granule compartments.

  View details for DOI 10.1242/dev.202284

  View details for Web of Science ID 001165385300004

  View details for PubMedID 38009921

  View details for PubMedCentralID PMC10753583

• Epitope tag-specific differences in the detection of COSA-1 marked crossover sites in C. elegans spermatocytes. microPublication biology Cahoon, C. K., Uebel, C. J., Villeneuve, A. M., Libuda, D. E. 2023; 2023

  Abstract

  Nascent crossover sites in C. elegans meiocytes can be cytologically detected using epitope-tagged versions of the pro-crossover protein COSA-1. In spermatocytes, differences exist between cytologically-detected and genetically-detected double crossover rates. Here, we examine nascent crossovers using both GFP- and OLLAS-tagged COSA-1. Similar to previous work, we find that most late pachytene spermatocytes display 5 COSA-1 foci, indicating one crossover per autosome bivalent. However, we detected more nuclei with >5 COSA-1 foci using OLLAS::COSA-1, reflecting some bivalents having 2 COSA-1 foci. These results demonstrate tag-specific differences in the detection of COSA-1 marked nascent crossovers in spermatocytes.

  View details for DOI 10.17912/micropub.biology.000724

  View details for PubMedID 36660421

• SIMR foci are found in the progenitor germ cells of C. elegans embryos. microPublication biology Uebel, C. J., Manage, K. I., Phillips, C. M. 2021; 2021

  Abstract

  RNA interference is a widely conserved mechanism of gene regulation and silencing across eukaryotes. In C. elegans, RNA silencing is coordinated through perinuclear nuage containing at least four granules: P granules, Z granules, Mutator foci, and SIMR foci. Embryonic localization of these granules is known for all except SIMR foci. Here we establish that SIMR foci first appear at the nuclear periphery in the P4 germline blastomere and become numerous and bright in the Z2 and Z3 progenitor germ cells. This timing coincides with the appearance or de-mixing of other germline granules, providing further evidence for coordinated germ granule reorganization.

  View details for DOI 10.17912/micropub.biology.000374

  View details for PubMedID 33644707

  View details for PubMedCentralID PMC7900827

• Mutator Foci Are Regulated by Developmental Stage, RNA, and the Germline Cell Cycle in Caenorhabditis elegans. G3 (Bethesda, Md.) Uebel, C. J., Agbede, D., Wallis, D. C., Phillips, C. M. 2020; 10 (10): 3719-3728

  Abstract

  RNA interference is a crucial gene regulatory mechanism in Caenorhabditis elegans Phase-separated perinuclear germline compartments called Mutator foci are a key element of RNAi, ensuring robust gene silencing and transgenerational epigenetic inheritance. Despite their importance, Mutator foci regulation is not well understood, and observations of Mutator foci have been largely limited to adult hermaphrodite germlines. Here we reveal that punctate Mutator foci arise in the progenitor germ cells of early embryos and persist throughout all larval stages. They are additionally present throughout the male germline and in the cytoplasm of post-meiotic spermatids, suggestive of a role in paternal epigenetic inheritance. In the adult germline, transcriptional inhibition results in a pachytene-specific loss of Mutator foci, indicating that Mutator foci are partially reliant on RNA for their stability. Finally, we demonstrate that Mutator foci intensity is modulated by the stage of the germline cell cycle and specifically, that Mutator foci are brightest and most robust in the mitotic cells, transition zone, and late pachytene of adult germlines. Thus, our data defines several new factors that modulate Mutator foci morphology which may ultimately have implications for efficacy of RNAi in certain cell stages or environments.

  View details for DOI 10.1534/g3.120.401514

  View details for PubMedID 32763952

  View details for PubMedCentralID PMC7534428

• A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in <i>C. elegans</i> ELIFE Manage, K., Rogers, A. K., Wallis, D. C., Liebel, C. J., Anderson, D. C., Nguyen, D. H., Arca, K., Brown, K. C., Rodrigues, R., de Albuquerque, B. M., Ketting, R. F., Montgomery, T. A., Phillips, C. 2020; 9

  Abstract

  piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, regulation of piRNA target genes is mediated by the mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, the steps between mRNA recognition by the piRNA pathway and siRNA amplification by the mutator complex are unknown. Here, we identify the Tudor domain protein, SIMR-1, as acting downstream of piRNA production and upstream of mutator complex-dependent siRNA biogenesis. Interestingly, SIMR-1 also localizes to distinct subcellular foci adjacent to P granules and Mutator foci, two phase-separated condensates that are the sites of piRNA-dependent mRNA recognition and mutator complex-dependent siRNA amplification, respectively. Thus, our data suggests a role for multiple perinuclear condensates in organizing the piRNA pathway and promoting mRNA regulation by the mutator complex.

  View details for DOI 10.7554/eLife.56731

  View details for Web of Science ID 000537741000001

  View details for PubMedID 32338603

  View details for PubMedCentralID PMC7255803

• Visualization and Quantification of Transposon Activity in Caenorhabditis elegans RNAi Pathway Mutants. G3 (Bethesda, Md.) Wallis, D. C., Nguyen, D. A., Uebel, C. J., Phillips, C. M. 2019; 9 (11): 3825-3832

  Abstract

  RNA silencing pathways play critical roles in maintaining quiescence of transposons in germ cells to promote genome integrity. However the precise mechanism by which different types of transposons are recognized by these pathways is not fully understood. Furthermore, the location in the germline where this transposition occurs after disruption of transposon silencing was previously unknown. Here we utilize the spatial and temporal organization of the Caenorhabditis elegans germline to demonstrate that transposition of DNA transposons in RNA silencing pathway mutants occur in all stages of adult germ cells. We further demonstrate that the double-strand breaks generated by transposons can restore homologous recombination in a mutant defective for the generation of meiosis-specific double-strand breaks. Finally, we detected clear differences in transposase expression and transposon excision between distinct branches of the RNA silencing pathway, emphasizing that there are multiple mechanisms by which transposons can be recognized and routed for small-RNA-mediated silencing.

  View details for DOI 10.1534/g3.119.400639

  View details for PubMedID 31533956

  View details for PubMedCentralID PMC6829131

• Phase-separated protein dynamics are affected by fluorescent tag choice. microPublication biology Uebel, C., Phillips, C. 2019; 2019

  View details for DOI 10.17912/micropub.biology.000143

  View details for PubMedID 32550421

  View details for PubMedCentralID PMC7252288

• 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 genetics Uebel, C. J., Anderson, D. C., Mandarino, L. M., Manage, K. I., Aynaszyan, S., Phillips, C. M. 2018; 14 (7): e1007542

  Abstract

  In C. elegans, efficient RNA silencing requires small RNA amplification mediated by RNA-dependent RNA polymerases (RdRPs). RRF-1, an RdRP, and other Mutator complex proteins localize to Mutator foci, which are perinuclear germline foci that associate with nuclear pores and P granules to facilitate small RNA amplification. The Mutator complex protein MUT-16 is critical for Mutator foci assembly. By analyzing small deletions of MUT-16, we identify specific regions of the protein that recruit other Mutator complex components and demonstrate that it acts as a scaffolding protein. We further determine that the C-terminal region of MUT-16, a portion of which contains predicted intrinsic disorder, is necessary and sufficient to promote Mutator foci formation. Finally, we establish that MUT-16 foci have many properties consistent with a phase-separated condensate and propose that Mutator foci form through liquid-liquid phase separation of MUT-16. P granules, which contain additional RNA silencing proteins, have previously been shown to have liquid-like properties. Thus, RNA silencing in C. elegans germ cells may rely on multiple phase-separated compartments through which sorting, processing, and silencing of mRNAs occurs.

  View details for DOI 10.1371/journal.pgen.1007542

  View details for PubMedID 30036386

  View details for PubMedCentralID PMC6072111