Biology subjects

Zhen, G.

Publications and source records attributed to Zhen, G..

6 recordsLinked to original sources

bioRxiv2022

Subcytoplasmic location of translation controls protein output

The cytoplasm is highly compartmentalized, but the extent and consequences of subcytopIasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endopIasmic reticuIum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on non-membrane protein-encoding mRNAs, we observed that 52% have a biased transcript distribution across these compartments. Compartment enrichment is determined by a combinatorial code based on mRNA length, exon length, and 3'UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentaIized by local translation environments.

molecular biology↗

bioRxiv2022

Transcription is ubiquitously terminated in thousands of bidirectional termination zones in yeast

Pervasive transcription of eukaryotic genomes requires intricate mechanisms to delineate boundaries for each transcriptional unit. How transcription is efficiently terminated before invading neighboring genes remains an open question. Here, after dissecting the cleavage and polyadenylation landscape using a hybrid approach, we observed thousands of bidirectional termination zones in the genome of Saccharomyces cerevisiae. These zones are [~]120 bp wide and terminate transcription from both sense and antisense strands in yeast. They are ubiquitously used as termination sites for both coding and non-coding genes. We suggest that the known transcription termination efficiency element, UAUAUA motifs, serves as the central elements in these zones. Notably, bidirectional termination zones are specifically nucleosome depleted, suggesting chromatin structure plays a key role in the formation of bidirectional termination zones in yeast. Finally, we provide evidence for transcriptional interference in these bidirectional termination zones, and expression level of each cleavage site is influenced by sequence contexts both upstream and downstream. We provide the first global fine-scale picture of transcription termination in a eukaryotic genome.

bioinformatics↗

bioRxiv2021

Quantification of alternative 3'UTR isoforms from single cell RNA-seq data with scUTRquant

Approximately half of human genes generate mRNA isoforms that differ in their 3'UTRs while encoding the same protein. 3'UTR and mRNA length is determined by 3' end cleavage sites (CS). Here, we mapped and categorized mRNA 3' end CS in more than 200 primary human and mouse cell types, resulting in a 40% increase of CS annotations relative to the GENCODE database. We incorporated these annotations into a novel computational pipeline, called scUTRquant, for rapid, precise, and accurate quantification of gene and 3'UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2,134 perturbations, we discovered extensive 3'UTR length changes across cell types that are as widespread and dynamically regulated as gene expression changes. Our data indicate that mRNA abundance and mRNA length are two independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.

bioinformatics↗

bioRxiv2021

Non-coding function for mRNAs in Focal Adhesion Architecture and Mechanotransduction

Messenger RNA (mRNA) compartmentalization within the cytosol is well-recognized as a key mechanism of local translation-mediated regulation of protein levels, but whether such localization could be a means of exercising non-coding mRNA function is unknown. Here, we explore non-coding functions for mRNAs associated with focal adhesions (FAs), cellular structures responsible for mediating cell adhesion and response to changes in the extracellular matrix (ECM). Using high-throughput single molecule imaging and genomic profiling approaches, we find that mRNAs with distinct sequence characteristics localize to FAs in different human cell types. Notably, [~]85% of FA-mRNAs are not translationally active at steady state or under conditions of FA dissolution or activation. Untranslated mRNA sequences are anchored to FA based on their functional states by the RNA binding protein, G3BP1, forming biomolecular granules. Removing RNA or G3BP1, but not blocking new polypeptide synthesis, dramatically changes FA protein composition and organization, resulting in loss of cell contractility and cellular ability to adapt to changing ECM. We have therefor uncovered a novel, non-coding role for mRNAs as scaffolds to maintain FA structure and function, broadening our understating of noncanonical mRNA functions.

cell biology↗

bioRxiv2020

Unstructured mRNAs form multivalent RNA-RNA interactions to generate TIS granule networks

The TIS granule network is a constitutively expressed membraneless organelle that concentrates mRNAs with AU-rich elements and interacts with the major site of protein synthesis, the rough endoplasmic reticulum. Most known biomolecular condensates are sphere-like, but TIS granules have a mesh-like morphology. Through in vivo and in vitro reconstitution experiments we discovered that this shape is generated by extensive intermolecular RNA-RNA interactions. They are mostly accomplished by mRNAs with large unstructured regions in their 3'UTRs that we call intrinsically disordered regions (IDRs). As AU-rich RNA is a potent chaperone that suppresses protein aggregation and is overrepresented in mRNAs with IDRs, our data suggests that TIS granules concentrate mRNAs that assist protein folding. In addition, the proximity of translating mRNAs in TIS granule networks may enable co-translational protein complex formation.

molecular biology↗

bioRxiv2017

Endosymbiont diversity and evolution across the weevil tree of life

As early as the time of Paul Buchner, a pioneer of endosymbionts research, it was shown that weevils host diverse bacterial endosymbionts, probably only second to the hemipteran insects. To date, there is no taxonomically broad survey of endosymbionts in weevils, which preclude any systematic understanding of the diversity and evolution of endosymbionts in this large group of insects, which comprise nearly 7% of described diversity of all insects. We gathered the largest known taxonomic sample of weevils representing four families and 17 subfamilies to perform a study of weevil endosymbionts. We found that the diversity of endosymbionts is exceedingly high, with as many as 44 distinct kinds of endosymbionts detected. We recovered an ancient origin of association of Nardonella with weevils, dating back to 124 MYA. We found repeated losses of this endosymbionts, but also cophylogeny with weevils. We also investigated patterns of coexistence and coexclusion.

evolutionary biology↗