Biology subjects

Tsagkris, S.

Publications and source records attributed to Tsagkris, S..

3 recordsLinked to original sources

bioRxiv2024

Pumilio differentially binds to mRNA 3' UTR isoforms to regulate localization of synaptic proteins

In neuronal cells, the regulation of RNA is crucial for the spatiotemporal control of gene expression, but how the correct localization, levels, and function of synaptic proteins are achieved is not well understood. In this study, we globally investigate the role of alternative 3 UTRs in regulating RNA localization in the synaptic regions of the Drosophila brain. We identify direct mRNA targets of the translational repressor Pumilio, finding that mRNAs bound by Pumilio encode proteins enriched in synaptosomes. Pumilio differentially binds to RNA isoforms of the same gene, favoring long, neuronal 3 UTRs. These longer 3 UTRs tend to remain in the neuronal soma, whereas shorter UTR isoforms localize to the synapse. In cultured pumilio mutant neurons, severe axon outgrowth defects were accompanied by mRNA isoform mislocalization, and proteins encoded by these Pumilio targets displayed excessive abundance at synaptic boutons. Our study identifies an important and widespread mechanism for the spatiotemporal regulation of protein function in neurons.

genomics↗

bioRxiv2024

ELAV mediates circular RNA biogenesis in neurons

Circular RNAs (circRNAs) arise from back-splicing of precursor RNAs and accumulate in the nervous system of animals, where they are thought to regulate gene expression and synaptic function. Here, we show that neuronal circRNA biosynthesis is mediated by the pan-neuronal RNA-binding protein ELAV. In Drosophila embryos, we characterize the circRNA landscape in normal and elav mutant neurons. We find that neuronal circRNAs are globally (>75%) depleted upon ELAV knockout, and induction of ELAV expression drives ectopic RNA circularization. In brain tissue, ELAV binds to pre-mRNA introns flanking putative circRNAs and decreases efficiency of linear splicing in favor of intron pairing at reverse complementary matches, inducing circularization. Together, our data demonstrate that ELAV directly modulates splicing decisions to generate the neuronal circRNA landscape.

molecular biology↗

bioRxiv2022

Systematic Epigenome Editing Captures the Context-dependent Instructive Function of Chromatin Modifications

Chromatin modifications are linked with regulating patterns of gene expression, but their causal role and context-dependent impact on transcription remains unresolved. Here, we develop a modular epigenome editing platform that programmes nine key chromatin modifications - or combinations thereof - to precise loci in living cells. We couple this with single-cell readouts to systematically quantitate the magnitude and heterogeneity of transcriptional responses elicited by each specific chromatin modification. Amongst these, we show installing H3K4me3 at promoters causally instructs transcription activation by hierarchically remodeling the chromatin landscape. We further dissect how DNA sequence motifs influence the transcriptional impact of chromatin marks, identifying switch-like and attenuative effects within distinct cis contexts. Finally, we examine the interplay of combinatorial modifications, revealing co-targeted H3K27me3 and H2AK119ub maximise silencing penetrance across single-cells. Our precision perturbation strategy unveils the causal principles of how chromatin modification(s) influence transcription, and dissects how quantitative responses are calibrated by contextual interactions.

synthetic biology↗