A5072324762- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Advanced NMR Techniques and Applications
- DNA and Nucleic Acid Chemistry
- Electron Spin Resonance Studies
- Magnetism in coordination complexes
- Genomics and Chromatin Dynamics
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Synthesis and Characterization of Heterocyclic Compounds
- Enzyme Structure and Function
- Influenza Virus Research Studies
- Force Microscopy Techniques and Applications
- RNA regulation and disease
- Protein Structure and Dynamics
European Molecular Biology Laboratory
2023-2024
European Molecular Biology Laboratory
2023-2024
European Bioinformatics Institute
2023
Stanford University
2017-2020
Scripps Research Institute
2017-2020
ETH Zurich
2007-2018
The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from ribosome binding site a subset mRNAs. Although we have previously described molecular basis high affinity RNA target bound to RsmE, it remains unknown how other lower targets are recognized same protein. Here, determined nuclear magnetic resonance solution structures five...
Structural information on RNA, emerging more and as a major regulator in gene expression, dramatically lags behind compared with proteins. Although NMR spectroscopy has proven to be an excellent tool solve RNA structures, it is hampered by the severe spectral resonances overlap found limiting its use for large molecules. Segmental isotope labeling of or ligation chemically synthesized containing modified nucleotides unmodified fragment have high potential overcoming current limitations...
The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and (1)H (13)C shifts. Statistics resonances from regularly Watson-Crick base-paired RNA revealed highly characteristic clusters. We developed two approaches using these statistics for double-stranded (dsRNA): manual approach that yields starting...
Cellular protein-RNA complexes assemble on nascent transcripts, but methods to observe transcription and protein binding in real time at physiological concentrations are not available. Here, we report a single-molecule approach based zero-mode waveguides that simultaneously tracks progress the of ribosomal S15 RNA transcripts during early ribosome biogenesis. We stable single RNAs immediately after for majority 35 °C less than half 20 °C. The remaining exhibit either rapid transient or...
Abstract The cyclooxygenase-2 is a pro-inflammatory and cancer marker, whose mRNA stability translation regulated by the CUG-binding protein 2 interacting with AU-rich sequences in 3′ untranslated region. Here, we present solution NMR structure of RRM3 complex 5′-UUUAA-3′ originating from COX-2 3′-UTR. We show that uses same binding surface moieties to interact AU- UG-rich RNA motifs, low high affinity, respectively. Using spectroscopy, isothermal titration calorimetry molecular dynamics...
Influenza A virus (IAV) exploits the host cellular machinery to facilitate its replication, yet many host-IAV interactions remain unexplored in context. Detailed information about interacting domains is also largely lacking. To address this, we employed in-cell cross-linking mass spectrometry (XL-MS) capture a vast network of protein-protein contact sites within IAV-infected human cells. This approach uncovered previously unrecognised factors, delineated steps hemagglutinin maturation...
Protein biosynthesis must be highly regulated to ensure proper spatiotemporal gene expression and thus cellular viability. Translation is often modulated at the initiation stage by RNA binding proteins through either promotion or repression of ribosome recruitment mRNA. However, it largely remains unknown how kinetics mRNA ribonucleoprotein (mRNP) assembly on untranslated regions (UTRs) relates its translation regulation activity. Using Sex-lethal (Sxl)-mediated msl-2 in female fly dosage...
Abstract A central question in biology is how macromolecular machines function cooperatively. In bacteria, transcription and translation occur the same cellular compartment can be physically functionally coupled. While several recently published high-resolution structures of ribosome-RNA polymerase (RNAP) complex provided first mechanistic insight into coupling process, we do not know these structural snapshots are placed along a dynamic reaction trajectory. Here, reconstitute complete...
Abstract Transcription of tRNA genes by RNA polymerase III requires the general transcription factor IIIC (TFIIIC), which recognizes intragenic A-box and B-box DNA motifs type II gene promoters. However, underlying mechanism has remained elusive, in part due to missing structural information for recognition. In this study, we use single-particle cryo-EM single-molecule FRET (smFRET) reveal real-time kinetic insights into how 520 kDa yeast TFIIIC complex engages A- context a promoter. Cryo-EM...
Ribosome assembly is one of the most fundamental processes in gene expression and has served as a playground to investigate molecular mechanisms how protein-RNA complexes (RNPs) assemble. The bacterial ribosome composed around 50 ribosomal proteins several which are co-transcriptionally assembled on ~4,500 nucleotides long pre-rRNA transcript that further processed modified during transcription, entire process taking 2 minutes vivo assisted by dozens factors. How this complex works so...
Transcription of transfer RNA (tRNA) genes by polymerase (Pol) III requires the general transcription factor IIIC (TFIIIC), which recognizes intragenic A-box and B-box DNA motifs type II gene promoters. However, underlying mechanism has remained elusive, in part due to missing structural information for recognition. In this study, we use single-particle cryogenic electron microscopy (cryo-EM) single-molecule fluorescence resonance energy (smFRET) reveal real-time kinetic insights into how...