Biology subjects

Rot, G.

Publications and source records attributed to Rot, G..

8 recordsLinked to original sources

bioRxiv2025

The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems

Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet--from the deep subsurface to the mountain tops--covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable SSU rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a long tail of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), both known and newly described species and communities can readily be placed into ecological context, taking full advantage of earlier work.

bioinformatics↗

bioRxiv2023

The Arabidopsis U1 snRNP regulates mRNA 3'-end processing

The removal of introns by the spliceosome is a key gene regulatory mechanism in eukaryotes, with the U1 snRNP subunit of the spliceosome playing a crucial role in the early stages of splicing. Studies in metazoans show that the U1 snRNP also conducts splicing-independent functions, but the lack of genetic tools and knowledge about U1 snRNP-associated proteins have limited the study of such splicing-independent functions in plants. Here, we describe an RNA-centric approach that identified more than 200 proteins associated with the Arabidopsis U1 snRNP, among them mRNA cleavage and polyadenylation factors. The loss of U1 core components is linked to premature cleavage and polyadenylation within gene bodies and alternative polyadenylation site selection in 3-UTRs. Overall, our work provides a comprehensive view of U1 snRNP interactors and reveals novel functions in regulating mRNA 3-end processing in Arabidopsis, thus establishing the groundwork for a better understanding of non-canonical functions of plant U1 snRNPs.

plant biology↗

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↗

bioRxiv2023

splicekit: a comprehensive toolkit for splicing analysis from short-read RNA-seq

MotivationAnalysis of alternative splicing using short-read RNA-seq data is a complex process that involves several steps: alignment of reads to the reference genome, identification of alternatively spliced features, motif discovery, analysis of RNA-protein binding near donor and acceptor splice sites, and exploratory data visualization. ResultsWe introduce splicekit, a python package that provides a comprehensive set of tools for conducting splicing analysis. Availability and implementationhttps://github.com/bedapub/splicekit and over PyPI.

bioinformatics↗

bioRxiv2022

Analysis of RNA polyadenylation in healthy and osteoarthritic human articular cartilage

An important transcript structural element is its 3 polyadenylated (polyA) tail, which defines the 3 boundary of the transcripts genetic information and is necessary for transcript stability. The position of the polyA tail can vary, with multiple alternatively polyadenylated (APA) transcripts existing for a single gene. This can lead to different length transcripts which can vary in their 3 regulatory domains and even by inclusion or exclusion of protein-coding introns. The distribution of polyA tail location on articular chondrocyte transcripts has not been examined before and this study aimed to be the first to define polyadenylation events in human chondrocytes using age-matched healthy and osteoarthritic knee articular cartilage samples. Total RNA was isolated from frozen tissue samples and analysed using the QuantSeqReverse 3 RNA Sequencing approach, where each read runs 3 to 5 from within the polyA tail into the transcript and will contains a distinct polyA site. Initial analysis of differential expression of overall transcript abundance identified by the reads showed significant disruption to transcript levels when healthy samples were compared to osteoarthritic ones. As we expected, differentially regulated genes were enriched with functionalities that were strongly associated with joint pathology. As part of this analysis, we also identified a substantial number of differentially expressed long non-coding RNAs that had not been linked to osteoarthritis before. Subsequent examination of polyA site data allowed us to deifne the extent of site usage across all the samples. This included identification of chondrocyte genes that exhibited the greatest amount polyA site variation. When comparing healthy and osteoarthritic samples, we found that differential use of polyadenylation sites was modest. However, of the small number of genes affected, there was clear potential for the change in polyadenylation site usage elicited by pathology to have functional relevance. We examined two genes, OSMR and KMT2A, in more detail, defining how APA affects transcript turnover and then, in the case of OSMR, identifying that APA is sensitive to inflammatory cytokine stimulation. Overall, we have characterised the polyadenylation landscape of human knee articular chondrocytes but can conclude that osteoarthritis does not elicit a widespread change in their polyadenylation site usage. This finding differentiates knee osteoarthritis from pathologies such as cancer where APA is more commonly observed.

molecular biology↗

bioRxiv2021

The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians

The eutherian placenta is a major site for parental genetic conflict. Here, we identify the X-linked Mbnl3 gene as a novel player in this dispute. Mbnl3 belongs to an RNA binding protein family whose members regulate alternative splicing and other aspects of RNA metabolism in association with cellular differentiation. We find that, in eutherians, Mbnl3 has become specifically expressed in placenta and has undergone accelerated sequence evolution leading to changes in its RNA binding specificities. Although its molecular roles are partly redundant with those of Mbnl2, Mbnl3 has also acquired novel biological functions. In particular, whereas Mbnl2;Mbnl3 double knockout mice display severe placental maturation defects leading to strong histological and functional abnormalities, Mbnl3 knockout alone results in increased placental growth and favors placental and fetal resource allocation during limiting conditions.

evolutionary biology↗

bioRxiv2020

A nuclear role for ARGONAUTE-2 in regulation of neuronal alternative polyadenylation

Argonaute 2 (AGO2), the effector protein partner of microRNAs (miRNAs) in the cytoplasmic RNA induced silencing complex, is further involved in nuclear RNA processing. However, a role for AGO2 in regulation of alternative polyadenylation was not yet demonstrated. Here, we reveal unexpected abundance of AGO2 in mouse neuronal nuclei and characterize nuclear AGO2 interactors by mass spectrometry. We discover that AGO2 broadly regulated alternative polyadenylation (APA) in neuronal cells. Specifically, we demonstrate how two isoforms of Ret mRNA, which encodes a receptor tyrosine kinase are regulated by AGO2-depenent APA, affecting downstream GDNF signaling in primary motor neurons.

cell biology↗

bioRxiv2020

A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells

Cells of many ectothermic species, including Drosophila melanogaster, maintain homeostatic function within a considerable temperature range. The cellular mechanisms enabling temperature acclimation are still poorly understood. At the transcriptional level, the heat shock response has been extensively analyzed. The opposite has received less attention. Here, using cultured Drosophila cells, we have identified genes with increased transcript levels at the lower end of the readily tolerated temperature range, as well as chromatin regions with increased DNA accessibility. Candidate cis-regulatory elements (CREs) for transcriptional upregulation at low temperature were selected and evaluated with a novel reporter assay for accurate assessment of their temperature-dependency. Robust transcriptional upregulation at low temperature could be demonstrated for a fragment from the pastrel gene, which expresses more transcript and protein at reduced temperatures. The CRE is controlled by the JAK/STAT signaling pathway and antagonizing activities of the transcription factors Pointed and Ets97D.

cell biology↗