A5083050853- RNA modifications and cancer
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Lipid metabolism and biosynthesis
- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- Bacterial Genetics and Biotechnology
- Advanced biosensing and bioanalysis techniques
- Cancer-related molecular mechanisms research
- DNA and Nucleic Acid Chemistry
- Cancer therapeutics and mechanisms
- Nuclear Structure and Function
- RNA Interference and Gene Delivery
- Biosensors and Analytical Detection
Yale University
2020-2025
Technische Universität Dresden
2019-2020
Bioengineering Center
2019
Dihydrouridine is a modified nucleotide universally present in tRNAs, but the complete dihydrouridine landscape unknown any organism. We introduce sequencing (D-seq) for transcriptome-wide mapping of D with single-nucleotide resolution and use it to uncover novel classes dihydrouridine-containing RNA yeast which include mRNA small nucleolar (snoRNA). The sites are concentrated conserved stem-loop regions consistent role folding many functional structures. demonstrate synthase (DUS)-dependent...
Merging of bridging staples with adjacent oligonucleotide sequences leads to a moderate increase DNA origami stability, while enzymatic ligation after assembly yields reinforced nanostructure superior stability at up 37 °C and in the presence 6 M urea.
Alternative polyadenylation (APA) is widespread among metazoans and has been shown to have important impacts on mRNA stability protein expression. Beyond a handful of well-studied organisms, however, its existence consequences not well investigated. We therefore turned the deep-branching red alga,
Polyadenylation controls mRNA biogenesis, nucleo-cytoplasmic export, translation and decay. These processes are interdependent coordinately regulated by poly(A)-binding proteins (PABPs), yet how PABPs themselves is not fully understood. Here, we report the discovery that human nuclear PABPN1 phosphorylated mitotic kinases at four specific sites during mitosis, a time when nucleoplasm cytoplasm mix. To understand functional consequences of phosphorylation, generated panel stable cell lines...
The cell nucleus contains distinct biomolecular condensates that form at specific genetic loci, organize chromosomes in 3D space, and regulate RNA processing. Among these, Cajal bodies (CBs) require key “scaffolding” proteins for their assembly, which is not fully understood. Here, we employ proximity biotinylation, mass spectrometry, functional screening to comprehensively identify test the functions of CB components. We document 144 protein interactors coilin, 70 were newly detected,...
The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain applicability, assumptions, limitations consequently, the efficacy precision they solve specific tasks. Therefore, there an increasing need for benchmarks, provision infrastructure continuous method evaluation. APAeval international community effort, organized by RNA Society in 2021, benchmark tools identification quantification usage alternative...
Summary An RNA’s catalytic, regulatory, or coding potential depends on RNA structure formation. Because base pairing occurs during transcription, early structural states can govern processing events and dictate the formation of functional conformations. These co-transcriptional remain unknown. Here, we develop CoSTseq, which detects nascent within upon exit from polymerases (Pols) transcriptome-wide in living yeast cells. By monitoring each nucleotide’s activity identify distinct classes...
Fluorescence microscopy has become a powerful tool in molecular cell biology. Visualizing specific proteins bacterial cells requires labeling with fluorescent or fluorogenic tags, preferentially at the native chromosomal locus to preserve expression dynamics associated genomic environment. Exploring protein function calls for targeted mutagenesis and observation of differential phenotypes. In model bacterium Escherichia coli, protocols tagging genes performing currently involve multiple...
Abstract In bacteria, the key mechanism governing mutation, adaptation and survival upon DNA damage is SOS response. Through autoproteolytic digestion triggered by single-stranded caused most antibiotics, transcriptional repressor LexA controls over 50 genes including repair pathways drivers of mutagenesis. Efforts to inhibit this response thereby combat antibiotic resistance rely on a broad understanding its behavior in vivo , which still limited. Here, we develop single-molecule...