A5040805189- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Genomics and Rare Diseases
- RNA and protein synthesis mechanisms
- MicroRNA in disease regulation
- Cancer Genomics and Diagnostics
- Poxvirus research and outbreaks
- Chromosomal and Genetic Variations
- Plant Virus Research Studies
- CRISPR and Genetic Engineering
- Advanced biosensing and bioanalysis techniques
- Statistical Methods and Inference
- Skin and Cellular Biology Research
- Genetic Syndromes and Imprinting
- Anesthesia and Neurotoxicity Research
- Gene expression and cancer classification
- Prenatal Screening and Diagnostics
- Tumors and Oncological Cases
- Molecular Biology Techniques and Applications
- Genetic Mapping and Diversity in Plants and Animals
- Dermatological and Skeletal Disorders
- Neuroinflammation and Neurodegeneration Mechanisms
University Medical Center of the Johannes Gutenberg University Mainz
2021-2025
Johannes Gutenberg University Mainz
2017-2025
Next generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes non-coding RNAs past years. However, reliable annotation extensive amounts data produced by high-throughput time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have number shortcomings including lack sensitivity under certain conditions, limited supported species or detectable sub-classes RNAs.Here we introduce unitas,...
PIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus protecting their genomes from detrimental insertion mutagenesis. Here, we reveal that genes piRNAs are ubiquitously expressed mollusks, similar to the situation arthropods. We describe lineage-specific adaptations of composition piRNA clusters great pond snail pacific oyster, likely reflecting differential gastropods bivalves. further show different with unique dynamically during oyster...
Direct RNA sequencing (DRS) is a nanopore-based technique for analyzing in its native form, promising breakthroughs diagnostics and biomarker development. Coupled to RNA002 chemistry, clinical implementation has been challenging due low throughput, accuracy, lack of large-scale RNA-modification models. In this study, we evaluate the improvements achieved by pairing latest RNA004 chemistry with novel modified-base-calling models pseudouridine N6-methyladenosine using diverse samples from cell...
<title>Abstract</title> Direct RNA sequencing (DRS) is a nanopore-based technique for analyzing in its native form, promising breakthroughs diagnostics and biomarker development. Coupled to RNA002 chemistry, clinical implementation has been challenging due low throughput, accuracy, lack of large-scale RNA-modification models. In this study, we evaluate the improvements achieved by pairing latest RNA004 chemistry with novel modified-base-calling models pseudouridine...
Fragments of mature tRNAs have long been considered as mere degradation products without physiological function. However, recent reports show that tRNA-derived small RNAs (tsRNAs) play prominent roles in diverse cellular processes across a wide spectrum species. Contrasting the situation other RNA pathways mechanisms behind these effects appear more diverse, complex, and are generally less well understood. In addition, surprisingly little is known about expression profiles tsRNAs different...
With the rise of Next-Generation-Sequencing (NGS) methods, Micro-RNAs (miRNAs) have achieved an important position in research landscape and been found to present valuable diagnostic tools various diseases such as multiple sclerosis or lung cancer. There is also emerging evidence that miRNAs play role pathogenesis neurodegenerative Alzheimer's disease (AD) Parkinson's (PD). Apparently, these come along with changes miRNA expression patterns which led attempts from researchers use small RNA...
The majority of Drosophila genes are expressed in a temperature-dependent manner, but the way which small RNAs may contribute to this effect is completely unknown as we currently lack an idea how RNA transcriptomes change function temperature. Applying high-throughput sequencing techniques complemented by quantitative real-time PCR experiments, demonstrate that altered ambient temperature induces drastic reversible changes sequence composition and total abundance both miRNA piRNA...
In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside known endemic areas. Setup proper genomic surveillance is utmost importance control such outbreaks. To this end, we performed Nanopore (PromethION P24) Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) sample. Adaptive sampling was applied for silico depletion host genome, allowing enrichment low abundance viral DNA without priori knowledge sample composition....
Abstract Adaptive nanopore sequencing as a diagnostic method for imprinting disorders and episignature analysis revealed an intragenic duplication of Exon 6 7 in UBE3A (NM_000462.5) patient with relatively mild Angelman-like syndrome. In all-in-one DNA hypomethylation the SNURF :TSS-DMR, known contributing deletions on maternal allele point mutations could be ruled out disease drivers. contrast, breakpoints orientation tandem clearly defined. Segregation family showed that derived de novo...
Upon chronic stress, a fraction of individuals shows stress resilience, which can prevent long-term mental dysfunction. The underlying molecular mechanisms are complex and have not yet been fully understood. In this study, we performed data-driven behavioural stratification together with single-cell transcriptomics the hippocampus in mouse model social defeat stress. Our work revealed that sub-group exhibiting responses upon dorsal is particularly involved neuroimmune responses,...
Abstract Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data different experimental backgrounds can introduce strong biases. In order to methodically investigate magnitude systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on genomic cohort 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) HiSeq, (iii) Complete...
Abstract PIWI proteins and a specific class of small non-coding RNAs, termed Piwi interacting RNAs (piRNAs), suppress transposon activity in animals on the transcriptional post-transcriptional level, thus protecting genomes from detrimental insertion mutagenesis. While vertebrates PIWI/piRNA system appears to be restricted germline, somatic expression piRNAs directed against transposons is widespread arthropods, likely representing ancestral state for this phylum. Here, we show that genes...
Genetic association studies have become increasingly important in unraveling the genetics of diseases or complex traits. Despite their value for modern genetics, conflicting conclusions often arise through difficulty confirming and replicating experimental results. We argue that this problem is largely based on application statistical relation measures are not appropriate genomic data analysis demonstrate standard used Genome-wide genomics linkage bear a statistic bias. This may come from...
Abstract In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside known endemic areas. Genomic surveillance is utmost importance control such outbreaks. To this end, we performed Nanopore Whole Genome Sequencing local sample on PromethION 24. Adaptive sampling was applied for silico depletion host genome, allowing enrichment low abundance viral DNA without priori knowledge composition. sequencing allowed high genome coverage,...
Mislabeling of cases as well controls in case-control studies is a frequent source strong bias prognostic and diagnostic tests algorithms. Common data processing methods available to the researchers biomedical community do not allow for consistent robust treatment labeled situations where both, case control groups, contain non-negligible proportion mislabeled instances. This an especially prominent issue regarding late-onset conditions, individuals who may convert populate group, screening...
Abstract Fragments of mature tRNAs have long been considered as mere degradation products without physiological function. However, recent reports show that tRNA fragments (tRFs) play prominent roles in diverse cellular processes across a wide spectrum species. Contrasting the situation other small RNA pathways mechanisms behind these effects appear more diverse, complex and are generally less well understood. In addition, surprisingly little is known about expression profiles tRFs different...
Brain homeostasis is the dynamic equilibrium whereby physiological parameters are kept actively within a specific range. The homeostatic range not fixed and may change throughout individual's lifespan, or be transiently modified in presence of severe perturbations. endocannabinoid system has emerged as safeguard homeostasis, e.g., it modulates neurotransmission protects neurons from prolonged excessively strong activation. We used genetically engineered mouse lines that lack cannabinoid...
Abstract Background Next generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes non-coding RNAs past years. However, reliable annotation extensive amounts data produced by high-throughput time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have number shortcomings including lack sensitivity under certain conditions, limited supported species or detectable sub-classes RNAs....
Abstract Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data different experimental backgrounds can introduce strong biases. In order to methodically investigate magnitude systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on genomic cohort 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) HiSeq, (iii) Complete...