A5026164683- RNA Research and Splicing
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA regulation and disease
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- Genomics and Chromatin Dynamics
- RNA Interference and Gene Delivery
- Circular RNAs in diseases
University of Würzburg
2024-2025
Goethe University Frankfurt
2021-2024
Institute of Molecular Biology
2023-2024
Abstract Ribonucleoprotein complexes are dynamic assemblies of RNA with RNA-binding proteins, which modulate the fate RNA. Inversely, riboregulates interactions and functions associated proteins. Dysregulation ribonucleoprotein is linked to diseases such as cancer neurological disorders. In dividing cells, proteins present in mitotic structures, but their impact on cell division remains unclear. By applying proteome-wide R-DeeP strategy cells synchronized mitosis versus interphase integrated...
Alternative splicing plays key roles for cell type–specific regulation of protein function. It is controlled by cis-regulatory RNA elements that are recognized binding proteins (RBPs). The MALT1 paracaspase a factor signaling pathways mediate innate and adaptive immune responses. critical controlling optimal T activation. We demonstrate depends on structural sequester the splice sites alternatively spliced exon7. RBPs hnRNP U L bind competitively to stem-loop structures involve 5′ 3′...
Abstract The RNA-binding protein PURA has been implicated in the rare, monogenetic, neurodevelopmental disorder Syndrome. binds both DNA and RNA associated with various cellular functions. Only little is known about its main roles molecular pathways affected upon depletion. Here, we show that predominantly located cytoplasm, where it to thousands of mRNAs. Many these transcripts change abundance response encoded proteins suggest a role for immune responses, mitochondrial function, autophagy...
Abstract MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs expected predominantly occur the 3′ untranslated region and involve perfect base-pairing of seed. Here, we generate a high-resolution map miR-181a/b-1 (miR-181) define targeting rules miR-181 developing murine T cells....
Abstract Summary Here, we introduce racoon_clip , a sustainable and fully automated pipeline for the complete processing of iCLIP eCLIP data to extract RNA binding signal at single-nucleotide resolution. is easy install execute, with multiple pre-settings customizable parameters, outputs conclusive summary report visualizations statistics all analysis steps. Availability Implementation implemented as snakemake-powered command line tool (snakemake version ≥ 7.22, Python 3.9). The latest...
Abstract Motivation A vast variety of biological questions connected to RNA-binding proteins can be tackled with UV crosslinking and immunoprecipitation (CLIP) experiments. However, the processing analysis CLIP data are rather complex. Moreover, different types experiments like iCLIP or eCLIP often processed in ways, reducing comparability between multiple Therefore, we aimed build an easy-to-use computational tool for that used both data, as well from other truncation-based methods. Results...
Abstract RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that yeast ribosome biogenesis factor Loc1p is an intrinsically disordered protein with eight repeating p ositively charged, u nstructured n ucleic acid binding (PUN) motifs. While a single these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In presence RNA, multivalent PUN drive phase separation....
Abstract Alternative splicing (AS) is a key layer of regulation in eukaryotic gene expression that investigated all areas life sciences. Differences AS between conditions can be quantified from transcriptome-wide short-read RNA sequencing (RNA-Seq) data with designated computational tools. However, not RNA-Seq are equally suited for analysis. Here, we perform an exemplary analysis to showcase the impact library characteristics on obtained results. Using three standard ENCODE datasets...
Abstract RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that yeast ribosome biogenesis factor Loc1p is an intrinsically disordered protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In presence RNA, multivalent PUN drive phase separation. Proteome-wide...
Abstract MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs expected predominantly occur the 3’ untranslated region and involve perfect base-pairing of seed. Here, we generate a high-resolution map miR-181a/b-1 (miR-181) define targeting rules miR-181 developing murine T-cells....
Abstract HnRNPs are ubiquitously expressed RNA-binding proteins, tightly controlling posttranscriptional gene regulation. Consequently, hnRNP networks essential for cellular homeostasis and their dysregulation is associated with cancer other diseases. However, the physiological function of hnRNPs in non-cancerous cell systems poorly understood. We analyzed importance HNRNPDL endothelial functions. Knockdown led to impaired proliferation, migration sprouting spheroids. Transcriptome analysis...
Abstract The RNA-binding protein PURA has been implicated in the rare, monogenetic, neurodevelopmental disorder Syndrome. binds both DNA and RNA associated with various cellular functions. Only little is known about its main roles molecular pathways affected upon depletion. Here, we show that predominantly located cytoplasm, where it to thousands of mRNAs. Many these transcripts change abundance response encoded proteins suggest a role for immune responses, mitochondrial function, autophagy...
ABSTRACT Alternative splicing is controlled by differential binding of trans -acting RNA proteins (RBPs) to cis -regulatory elements in intronic and exonic pre-mRNA regions 1-3 . How secondary structure the transcripts affects recognition RBPs determines alternative exon usage poorly understood. The MALT1 paracaspase a key component signaling pathways that mediate innate adaptive immune responses 4 exon7 critical for controlling optimal T cell activation 5,6 Here, we demonstrate processing...