Biology subjects

Weidmann, C.

Publications and source records attributed to Weidmann, C..

4 recordsLinked to original sources

bioRxiv2026

Robust mammalian RNA localization elements are complex and multipartite

The subcellular localization patterns of RNAs are controlled by regulatory elements contained within them. However, for most localized RNAs, the identities of these elements remain unknown. We had previously identified several localization elements that are necessary and sufficient for robust, kinesin-dependent RNA targeting to microtubule plus ends in a variety of cell types. Yet the characteristics of these elements that are critical for function remained unclear. To address this, we systematically created tens of thousands of mutant localization elements and quantified their ability to regulate subcellular RNA localization in neuronal cells. We found that the minimally active size of these localization elements is large, approximately 200 nucleotides. These elements contain multiple important subsequences, with some being completely intolerant of any changes and others being tolerant to a shuffling of nucleotide order but not to changes in nucleotide composition. Using single molecule microscopy, we verified these findings in primary rat neurons. Together, these results demonstrate that highly active mammalian RNA localization elements are large, complex, and multipartite and lay a foundation for further mechanistic studies of their function.

molecular biology↗

bioRxiv2025

Cytoplasmic localization of PUS7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance

Pseudouridine ({Psi}) is an abundant post-transcriptional modification found across all classes of RNA. It has been widely speculated that {Psi} inclusion in mRNAs might provide an avenue for cells to control gene expression post-transcriptionally. Here we demonstrate that one of the principal mRNA pseudouridylating enzymes, pseudouridine synthase 7 (PUS7), exhibits a stress-induced accumulation in the cytoplasm of yeast and human epithelial lung cells. Stress-induced and cytoplasmic localization of PUS7 promote {Psi}-incorporation into hundreds of mRNA targets. Furthermore, engineered PUS7 cytoplasmic localization increases cellular fitness under ROS and divalent metal ion stress. Consistent with this, transcripts modified upon PUS7 cytoplasmic localization are enriched within mRNAs encoding proteins involved in divalent metal metabolism and ROS stress pathways. In contrast, tRNA sites modified by PUS7 ({Psi}13 and {Psi}35 are unperturbed). Quantitative proteomics reveal a reshaping of the proteome upon PUS7 relocalization under stress, with proteins involved in metal and ROS homeostasis being particularly sensitive to PUS7 localization. Collectively, our data demonstrate that PUS7 localization alters mRNA pseudouridylation patterns to modulate protein production and enhance cellular fitness.

biochemistry↗

bioRxiv2022

Structural conservation of MALAT1 long non-coding RNA in cells and in evolution

Although not canonically polyadenylated, the long non-coding RNA MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) is stabilized by a highly conserved 159 nucleotide triple helix structure on its 3 end. The entire MALAT1 transcript is over 8,000 nucleotides long in humans and is considered one of the most conserved lncRNAs, at both the sequence and structure levels. The strongest structural conservation signal (as measured by co-variation of base-pairs) is in the triple helix structure. Primary sequence analysis of co-variation alone cannot confirm the degree of structural conservation of the entire full-length transcript. Furthermore, RNA structure is often context dependent; RNA binding proteins that are differentially expressed in different cell types may alter structure. We investigate here the in cell and cell free structures of the full-length human and green monkey (Chlorocebus sabaeus) MALAT1 transcripts in multiple tissue-derived cell lines using SHAPE chemical probing. Our data reveals surprising levels of uniform structural conservation in different cell lines, in cells and cell free, and even between species, despite significant differences in primary sequence. The uniformity of the structural conservation across the entire transcript suggests that, despite seeing co-variation signals only in the three-helix junction of the lncRNA, the rest of the transcripts structure is remarkably conserved at least in primates and across multiple cell types and conditions.

molecular biology↗

bioRxiv2017

mRNA structure determines specificity of a polyQ-driven phase separation

RNA promotes liquid-liquid phase separation (LLPS) to build membrane-less compartments in cells. How distinct molecular compositions are established and maintained in these liquid compartments is unknown. Here we report that secondary structure allows mRNAs to self-associate and determines if an mRNA is recruited to or excluded from liquid compartments. The polyQ-protein Whi3 induces conformational changes in RNA structure and generates distinct molecular fluctuations depending on the RNA sequence. These data support a model in which structure-based, RNA-RNA interactions promote assembly of distinct droplets and protein-driven, conformational dynamics of the RNA maintain this identity. Thus, the shape of RNA can promote the formation and coexistence of the diverse array of RNA-rich liquid compartments found in a single cell.\n\nOne Sentence SummaryIdentity in cellular, phase-separated compartments arises from RNA-RNA complexes encoded by mRNA secondary structures.

cell biology↗