Biology subjects

Zibara, K.

Publications and source records attributed to Zibara, K..

5 recordsLinked to original sources

bioRxiv2025

Cell heterogeneity contributes to the variable response of HIV-1 to latency reversing agents

Transcriptional noise contributes to gene expression variability, but its origin and impact in HIV-1 latency remain incompletely characterized. Here, we combine a dual-copy MS2-tagging system with novel mathematical analysis to investigate the variability of HIV-1 transcription in live cells. In the basal state, the transcriptional activity of proviruses located in the same cell was uncorrelated, indicating that expression variability primarily comes from the intrinsic stochasticity of promoter dynamics. Upon stimulation with diverse latency-reversing agents, viral transcription became more correlated within cells than across them, revealing a shift from promoter-driven to cell state-driven variability. Analysis of the molecular drug targets confirmed variable effects across cells. Our findings indicates that cellular heterogeneity shapes the response to latency reversing agents and demonstrate how quantitative tools can dissect noise sources. This work offers mechanistic insights into HIV-1 latency and informs strategies to target the latent viral reservoir. TeaserLive transcription imaging reveals how cell heterogeneity contributes to the variability of HIV-1 activation.

molecular biology↗

bioRxiv2024

Co-translational sorting enables a single mRNA to generate distinct polysomes with different localizations and protein fates

{beta}-catenin is a multi-functional protein playing essential roles in tissue homeostasis and cancer. It bridges E-cadherin to the cytoskeleton and also activates transcription in response to Wnt. Plasma membrane {beta}-catenin is stable whereas without Wnt, cytoplasmic {beta}-catenin is degraded by the destruction complex, composed of APC and Axin. Here, we show that APC and Axin associate with many mRNAs and that this occurs via the nascent protein chains. Notably, APC and Axin bind {beta}-catenin mRNAs present as either single polysome or polysome condensates, and co-translational interactions constitute the major fraction of their binding to the {beta}-catenin protein. Remarkably, E-cadherin also binds {beta}-catenin co-translationally, and {beta}-catenin mRNAs localize either with APC in the cytosol or E-cadherin at the plasma membrane. Thus, co-translational interactions sort {beta}-catenin mRNAs into distinct polysome populations that spatially segregate in cells and synthesize proteins with different functions. Co-translational polysome sorting provides a mechanism to regulate the fate of multi-functional proteins.

molecular biology↗

bioRxiv2020

The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions

RNA localization and local translation are important for numerous cellular functions. In mammals, a class of mRNAs localize to cytoplasmic protrusions in an APC-dependent manner, with roles during cell migration. Here, we investigated this localization mechanism. We found that the KIF1C motor interacts with APC-dependent mRNAs and is required for their localization. Live cell imaging revealed rapid, active transport of single mRNAs over long distances that requires both microtubules and KIF1C. Two color imaging directly showed single mRNAs transported by single KIF1C motors, with the 3UTR being sufficient to trigger KIF1C-dependent RNA transport and localization. Moreover, KIF1C remained associated with peripheral, multimeric RNA clusters and was required for their formation. These results reveal an RNA transport pathway in mammalian cells, in which the KIF1C motor has a dual role both in transporting RNAs and in promoting their clustering within cytoplasmic protrusions. Interestingly, KIF1C also transports its own mRNA suggesting a possible feedback loop acting at the level of mRNA transport.

cell biology↗

bioRxiv2020

A conserved choreography of mRNAs at centrosomes reveals a localization mechanism involving active polysome transport

Local translation allows for a spatial control of gene expression. Here, we used high-throughput smFISH to screen centrosomal protein-coding genes, and we describe 8 human mRNAs accumulating at centrosomes. These mRNAs localize at different stages during cell cycle with a remarkable choreography, indicating a finely regulated translational program at centrosomes. Interestingly, drug treatments and reporter analyses revealed a common translation-dependent localization mechanism requiring the nascent protein. Using ASPM and NUMA1 as models, single mRNA and polysome imaging revealed active movements of endogenous polysomes towards the centrosome at the onset of mitosis, when these mRNAs start localizing. ASPM polysomes associate with microtubules and localize by either motor-driven transport or microtubule pulling. Remarkably, the Drosophila orthologs of the human centrosomal mRNAs also localize to centrosomes and also require translation. These data identify a conserved family of centrosomal mRNAs that localize by active polysomes transport mediated by nascent proteins.

cell biology↗

bioRxiv2020

A localization screen reveals translation factories and widespread co-translational RNA targeting

Local translation allows a spatial control of gene expression. Here, we performed a dual protein/mRNA localization screen, using smFISH on 523 human cell lines expressing GFP-tagged genes. A total of 32 mRNAs displayed specific cytoplasmic localizations, and we observed local translation at unexpected locations, including cytoplasmic protrusions, cell edges, endosomes, Golgi, the nuclear envelope and centrosomes, the latter being cell cycle dependent. Quantitation of mRNA distribution and automatic pattern classification revealed a high degree of localization heterogeneity between cells. Surprisingly, mRNA localization frequently required ongoing translation, indicating widespread co-translational RNA targeting. Interestingly, while P-body accumulation was frequent (15 mRNAs), four mRNAs accumulated in foci that were distinct structures. These foci lacked the mature protein, but nascent polypeptide imaging showed that they were specialized translation factories. For {beta}-catenin, foci formation was regulated by Wnt, relied on APC-dependent polysome aggregation, and led to nascent protein degradation. Thus, translation factories uniquely regulate nascent protein metabolism and create a fine granular compartmentalization of translation.

cell biology↗