Biology subjects

Cohen-Fix, O.

Publications and source records attributed to Cohen-Fix, O..

4 recordsLinked to original sources

bioRxiv2025

Kar4 acts as a Ste12 regulator in Saccharomyces cerevisiae, promoting Ste12 binding to a specific DNA motif genome-wide

Kar4 is a putative transcription factor required for efficient mating in the budding yeast Saccharomyces cerevisiae. Kar4 functions with Ste12, the master transcriptional regulator of the yeast mating pheromone response, to promote the transcription of a subset of Ste12 targets required for mating. However, the mechanism by which Kar4 modulates Ste12 activity has remained uncertain. Here, we examined Kar4s function at the levels of transcription (RNA-seq) and Ste12 DNA binding (ChIP-exo). We show that Kar4 promotes Ste12 binding to nearly all Ste12 DNA-binding sites associated with transcriptionally-upregulated genes, even if their upregulation is not dependent on Kar4. We further found that the majority of Ste12-binding sites have two pheromone response elements (PREs) separated by four nucleotides in a head-to-tail orientation (H-T 4 motif). Sites associated with Kar4-dependent transcription have PREs with more mismatches and substantially lower Ste12 occupancy in kar4{Delta} cells than sites linked to Kar4-independent transcription. During the pheromone response in kar4{Delta} cells, Ste12 exhibits increased binding to non-H-T 4 motifs, particularly T-T 3 motifs, resulting in the abnormal upregulation of many genes not transcribed during the wild-type pheromone response. Therefore, we propose that Kar4 functions by increasing the DNA-binding specificity of Ste12 globally, promoting its binding primarily to H-T 4 motifs. Our model is consistent with previously-observed slower induction kinetics of Kar4-dependent genes via a feed-forward mechanism. Lastly, we uncovered several novel aspects of the pheromone response, including a broad role for the Crz1 transcription factor, induction of stress responses, and the identification of pheromone-responsive intergenic transcripts.

genetics↗

bioRxiv2025

The centriculum, a membrane that surrounds C. elegans centrosomes, acts as a microtubule filter

Centrosomes are cytoplasmic microtubule-nucleating structures. They are considered membraneless organelles, but in several cell types they are surrounded by ER-derived membrane. In C. elegans early embryos, this membrane forms a dense membrane reticulum, named the centriculum, that affects centrosome structure and microtubule nucleating capacity. The centriculum is adjacent to the centrosomes pericentriolar material (PCM) and to abundant, short peri-centrosomal microtubules. Here we show that when microtubule abundance is reduced, centriculum and PCM size decrease, while the density of the PCM protein SPD-5 increases, suggesting that the PCM can be compacted. We further show that centriculum size is determined by microtubules, and that the centriculum likely limits the length of peri-centrosomal microtubules. Finally, we find that the centriculum is more porous where spindle microtubules pass compared to where astral microtubules pass. These data are consistent with the centriculum serving as a microtubule filter, blocking the extension of most, but not all, centrosome-nucleated microtubules. Finally, if microtubule-centriculum collisions result in microtubule catastrophe, the filter function of the centriculum could also explain the high concentration of soluble tubulin at the C. elegans centrosome. Summary StatementThe centriculum is a centrosome-associated membrane reticulum in C. elegans embryos. This study shows that its size depends on microtubules and that it may act as a filter, limiting microtubule growth.

cell biology↗

bioRxiv2022

The Caenorhabditis elegans centrosome is surrounded by a membrane reticulum, the centriculum, that affects centrosome size and function

Centrosomes are membraneless organelles that nucleate microtubules. At their core is a pair of centrioles that recruit pericentriolar material (PCM), a phase-separated condensate. In many cell types, including human cells, centrosomes are surrounded by endoplasmic reticulum-derived membranes of unknown structure and function. Using volume electron microscopy, we show that the C. elegans centrosome is surrounded by a membrane reticulum that we call the centriculum, for centrosome-associated membrane reticulum. Increasing centriculum size by genetic means led to expansion of the PCM and increased microtubule nucleation capacity, an unexpected finding given that the PCM is a membraneless condensate. We provide evidence that the centriculum serves as a microtubule "filter" by limiting the number of microtubules that can elongate fully. We also show the centriculum fuses with the nuclear envelope during mitosis. We propose that this fusion contributes to nuclear envelope breakdown by transducing forces from the elongating spindle to the nuclear membranes.

cell biology↗

bioRxiv2021

An RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans reveals the involvement of unexpected processes

Aberration in nuclear morphology is one of the hallmarks of cellular transformation. However, the processes that, when mis-regulated, result aberrant nuclear morphology are poorly understood. In this study we carried out a systematic, high-throughput RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans embryos. The screen employed over 1700 RNAi constructs against genes required for embryonic viability. Nuclei of early embryos are typically spherical and their NPCs are evenly distributed. The screen was performed on early embryos expressing a fluorescently tagged component of the nuclear pore complex (NPC), allowing visualization of nuclear shape as well as the distribution of NPCs around the nuclear envelope. Our screen uncovered 182 genes whose down-regulation resulted in one or more abnormal nuclear phenotypes, including multiple nuclei, micronuclei, abnormal nuclear shape, anaphase bridges and abnormal NPC distribution. Many of these genes fall into common functional groups, including some that were not previously known to affect nuclear morphology, such as genes involved in mitochondrial function, the vacuolar ATPase and the CCT chaperonin complex. The results of this screen add to our growing knowledge of processes that affect nuclear morphology and that may be altered in cancer cells that exhibit abnormal nuclear shape.

cell biology↗