Biology subjects

Fansler, M. M.

Publications and source records attributed to Fansler, M. M..

3 recordsLinked to original sources

bioRxiv2023

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, and limitations and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3'-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for seamless extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies. Furthermore, the containers and reproducible workflows generated in the course of this project can be seamlessly deployed and extended in the future to evaluate new methods or datasets.

bioinformatics↗

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↗

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↗