Biology subjects

Medley, J. C.

Publications and source records attributed to Medley, J. C..

8 recordsLinked to original sources

bioRxiv2025

3' Nucleotide Asymmetry Directs miRNA Strand Selection

Accurate microRNA (miRNA) strand selection is essential for defining the regulatory landscape of the miRNA-induced silencing complex (miRISC). While 5' nucleotide identity and duplex thermodynamics have been proposed to bias strand choice, these features cannot fully explain in vivo strand preferences. Here, we uncover a conserved and previously unrecognized role for 3' nucleotide asymmetry in directing miRNA strand selection in Caenorhabditis elegans and human cells. A favorable 3' terminal nucleotide on the passenger strand promotes selective loading of the opposing guide strand into miRISC, revealing a cooperative interplay between 5' and 3' terminal asymmetries that ensures precise strand discrimination. These findings establish a unified, evolutionarily conserved mechanism for miRNA duplex sorting and expand the fundamental rules governing small RNA biogenesis.

molecular biology↗

bioRxiv2025

In silico unwinding of Caenorhabditis elegans microRNA duplexes to evaluate thermodynamic end stabilities improves predictions of microRNA strand selection

microRNAs (miRNAs) are endogenous [~]22 nucleotide long, non-coding RNAs that post-transcriptionally regulate gene expression. During miRNA biogenesis, stem-loop-containing miRNA precursors are enzymatically cleaved to form a small RNA duplex. Cleavage positions are determined based on the position of structural motifs and junctions on the stem-loop precursor. The duplex end containing a favorable 5 nucleotide and lower thermodynamic stability is subsequently loading into an Argonaute protein. Typically, one duplex (guide) strand is retained in Argonaute and becomes functional whereas the other (passenger) strand is degraded. Therefore, accurate structural predictions of miRNA intermediates and quantification of duplex end stabilities are important towards understanding miRNA biogenesis. Here, we compiled predicted secondary structures for all Caenorhabditis elegans miRNA hairpins and duplexes at physiologically relevant temperatures. We developed a new approach to calculate the thermodynamic stability of miRNA duplex ends, which resulted in improved predictions of miRNA strand selection. Our approach introduces hard constraints to folding algorithms to restrict base-paring of terminal nucleotides, which improves modeling of in vivo duplex end unwinding. We propose that constrained RNA folding can be used to evaluate local stabilities within an RNA secondary structure.

genetics↗

bioRxiv2025

LIN-67 functionally interacts with heterochronic miRNAs and regulates developmental timing in Caenorhabditis elegans

Temporal regulation of gene expression is required for developmental transitions, including differentiation, proliferation, and morphogenesis. In the nematode Caenorhabditis elegans, heterochronic microRNAs (miRNAs) regulate the temporal expression of genes that promote animal development. The heterochronic miRNAs lin-4 and let-7 are required during different stages of larval development and are associated with the miRNA-specific Argonaute ALG-1. In this study, we have identified lin-67 as a heterochronic gene that negatively regulates lin-4, let-7, and alg-1. Loss of lin-67 function restores proper developmental timing and stage-specific gene expression to hypomorphic lin-4 and let-7 mutants. We found that loss of lin-67 resulted in a reduced number of seam cells, defects in alae formation, precocious expression of an adult-specific gene reporter, and sterility. LIN-67 contains a K homology (KH) RNA-binding domain and is a homolog of the Sam68-like splicing factor KHDRBS2. We show that LIN-67 localizes to the nucleus throughout animal development and is enriched in nuclear foci. Mutating the KH domain of LIN-67 abolished the nuclear localization of LIN-67, suggesting that the localization of LIN-67 is likely dependent on RNA-binding activity. We show that LIN-67 negatively regulates lin-4 miRNA levels and restores normal levels of let-7 to alg-1 mutants, which can, at least in part, explain how lin-67 suppresses alg-1. Our data indicate that lin-67 is a novel heterochronic gene that regulates developmental timing and miRNA-dependent gene regulation in C. elegans.

developmental biology↗

bioRxiv2023

Site-Specific Phosphorylation of ZYG-1 Regulates ZYG-1 Stability and Centrosome Number

Spindle bipolarity is critical for genomic integrity. Given that centrosome number often dictates mitotic bipolarity, tight control of centrosome assembly is vital for the fidelity of cell division. The kinase ZYG-1/Plk4 is a master centrosome factor that is integral for controlling centrosome number and is modulated by protein phosphorylation. While autophosphorylation of Plk4 has been extensively studied in other systems, the mechanism of ZYG-1 phosphorylation in C. elegans remains largely unexplored. In C. elegans, Casein Kinase II (CK2) negatively regulates centrosome duplication by controlling centrosome-associated ZYG-1 levels. In this study, we investigated ZYG-1 as a potential substrate of CK2 and the functional impact of ZYG-1 phosphorylation on centrosome assembly. First, we show that CK2 directly phosphorylates ZYG-1 in vitro and physically interacts with ZYG-1 in vivo. Intriguingly, depleting CK2 or blocking ZYG-1 phosphorylation at putative CK2 target sites leads to centrosome amplification. In the non-phosphorylatable (NP)-ZYG-1 mutant embryo, the overall levels of ZYG-1 are elevated, leading to an increase in centrosomal ZYG-1 and downstream factors, providing a possible mechanism of the NP-ZYG-1 mutation to drive centrosome amplification. Moreover, inhibiting the 26S proteasome blocks degradation of the phospho-mimetic (PM)-ZYG-1, while the NP-ZYG-1 mutant shows partial resistance to proteasomal degradation. Our findings suggest that site-specific phosphorylation of ZYG-1, partly mediated by CK2, controls ZYG-1 levels via proteasomal degradation, limiting centrosome number. We provide a mechanism linking CK2 kinase activity to centrosome duplication through direct phosphorylation of ZYG-1, which is critical for the integrity of centrosome number.

cell biology↗

bioRxiv2021

Single Nucleotide Substitutions Effectively Block Cas9 and Allow for Scarless Genome Editing in Caenorhabditis elegans

In Caenorhabditis elegans, germline injection of Cas9 complexes is reliably used to achieve genome editing through homology-directed repair of Cas9-generated DNA breaks. To prevent Cas9 from targeting repaired DNA, additional blocking mutations are often incorporated into homologous repair templates. Cas9 can be blocked either by mutating the PAM sequence that is essential for Cas9 activity or by mutating the guide sequence that targets Cas9 to a specific genomic location. However, it is unclear how many nucleotides within the guide sequence should be mutated, since Cas9 can recognize "off-target" sequences that are imperfectly paired to its guide. In this study, we examined whether single-nucleotide substitutions within the guide sequence are sufficient to block Cas9 and allow for efficient genome editing. We show that a single mismatch within the guide sequence effectively blocks Cas9 and allows for recovery of edited animals. Surprisingly, we found that a low rate of edited animals can be recovered without introducing any blocking mutations, suggesting a temporal block to Cas9 activity in C. elegans. Furthermore, we show that the maternal genome of hermaphrodite animals is preferentially edited over the paternal genome. We demonstrate that maternally provided haplotypes can be selected using balancer chromosomes and propose a method of mutant isolation that greatly reduces screening efforts post-injection. Collectively, our findings expand the repertoire of genome editing strategies in C. elegans and demonstrate that extraneous blocking mutations are not required to recover edited animals when the desired mutation is located within the guide sequence.

genetics↗

bioRxiv2020

APC/CFZR-1 Controls ZYG-1 Levels to Regulate Centrosome Assembly

Aberrant centrosome numbers are associated with human cancers. The levels of centrosome regulators positively correlate with centrosome number. Thus, tight control of centrosome protein levels is critical. In Caenorhabditis elegans, the anaphase-promoting complex/cyclosome and co-activator FZR-1 (APC/CFZR-1) ubiquitin ligase negatively regulates centrosome assembly through SAS-5 degradation. In this study, we identify the C. elegans ZYG-1 (Plk4 in human) as a new substrate of APC/CFZR-1. Inhibiting APC/CFZR-1 or mutating a ZYG-1 destruction (D)-box leads to elevated ZYG-1 levels at centrosomes, restoring bipolar spindles and embryonic viability to zyg-1 mutants, suggesting that APC/CFZR-1 targets ZYG-1 for proteasomal degradation via D-box motif. We also show the Slimb/{beta}TrCP-binding (SB) motif is critical for ZYG-1 degradation, substantiating a conserved mechanism by which ZYG-1/Plk4 stability is regulated by SCFSlimb/{beta}TrCP-dependent proteolysis via the conserved SB motif in C. elegans. Furthermore, inhibiting both APC/CFZR-1 and SCFSlimb/{beta}TrCP, by co-mutating ZYG-1 SB and D-box motifs, stabilizes ZYG-1 in an additive manner, conveying that APC/CFZR-1 and SCFSlimb/{beta}TrCP ubiquitin ligases function cooperatively for timely ZYG-1 destruction in C. elegans embryos where ZYG-1 activity remains at threshold level to ensure normal centrosome number.

cell biology↗

bioRxiv2017

APC/CFZR-1 Controls SAS-5 Levels to Regulate Centrosome Duplication in Caenorhabditis elegans

As the primary microtubule-organizing center, centrosomes play a key role in establishing mitotic bipolar spindles that secure correct transmission of genomic content. For the fidelity of cell division, centrosome number must be strictly controlled by duplicating only once per cell cycle. Proper levels of centrosome proteins are shown to be critical for normal centrosome number and function. Overexpressing core centrosome factors leads to extra centrosomes, while depleting these factors results in centrosome duplication failure. In this regard, protein turnover by the ubiquitin-proteasome system provides a vital mechanism for the regulation of centrosome protein levels. Here, we report that FZR-1, the Caenorhabditis elegans homolog of Cdh1/Hct1/Fzr, a co-activator of the anaphase promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase, functions as a negative regulator of centrosome duplication in the Caenorhabditis elegans embryo. During mitotic cell division in the early embryo, FZR-1 is associated with centrosomes and enriched at nuclei. Loss of fzr-1 function restores centrosome duplication and embryonic viability to the hypomorphic zyg-1(it25) mutant, in part, through elevated levels of SAS-5 at centrosomes. Our data suggest that the APC/CFZR-1 regulates SAS-5 levels by directly recognizing the conserved KEN-box motif, contributing to proper centrosome duplication. Together, our work shows that FZR-1 plays a conserved role in regulating centrosome duplication in Caenorhabditis elegans.

genetics↗

bioRxiv2016

Casein Kinase II is Required for Proper Cell Division and Acts as a Negative Regulator of Centrosome Duplication in C. elegans Embryos

Summary statementThe conserved protein kinase CK2 negatively regulates centrosome assembly and is required for proper cell cycle progression and cytokinesis in early C. elegans embryos.\n\nAbstractCentrosomes are the primary microtubule-organizing centers that orchestrate microtubule dynamics during the cell cycle. The correct number of centrosomes is pivotal for establishing bipolar mitotic spindles that ensure accurate segregation of chromosomes. Thus, centrioles must duplicate once per cell cycle, one daughter per mother centriole, the process of which requires highly coordinated actions among core factors and modulators. Protein phosphorylation is shown to regulate the stability, localization and activity of centrosome proteins. Here, we report the function of Casein Kinase II (CK2) in early C. elegans embryos. The catalytic subunit (KIN-3/CK2) of CK2 localizes to nuclei, centrosomes and midbodies. Inactivating CK2 leads to cell division defects, including chromosome missegregation, cytokinesis failure and aberrant centrosome behavior. Furthermore, depletion or inhibiting kinase activity of CK2 results in elevated ZYG-1 levels at centrosomes, restoring centrosome duplication and embryonic viability to zyg-1 mutants. Our data suggest that CK2 functions in cell division and negatively regulates centrosome duplication in a kinase-dependent manner.

cell biology↗