A5013264305- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Fuel Cells and Related Materials
- Cancer-related molecular mechanisms research
- RNA regulation and disease
- CRISPR and Genetic Engineering
- Bacterial Genetics and Biotechnology
- Educational Strategies and Epistemologies
- Genomics and Phylogenetic Studies
- Viral Infections and Immunology Research
- Advanced biosensing and bioanalysis techniques
- HVDC Systems and Fault Protection
- Peptidase Inhibition and Analysis
- Cancer-related gene regulation
- Bacteriophages and microbial interactions
- SARS-CoV-2 and COVID-19 Research
- Genomics and Chromatin Dynamics
- Innovative Teaching Methods
- Fungal and yeast genetics research
- Cancer therapeutics and mechanisms
- Virus-based gene therapy research
- DNA and Nucleic Acid Chemistry
- RNA Interference and Gene Delivery
- Science Education and Pedagogy
University of Michigan
2009-2024
The University of Texas at Austin
2024
Michigan United
2022
Xiaomi (China)
2015
Ross School
2015
Johns Hopkins University
2014-2015
Johns Hopkins Medicine
2015
Chemical modifications of RNAs have long been established as key modulators nonprotein-coding RNA structure and function in cells. There is a growing appreciation that messenger (mRNA) sequences responsible for directing protein synthesis can also be posttranscriptionally modified. The enzymatic incorporation mRNA has many potential outcomes, including changing stability, recruitment, translation. We tested how one the most common present coding regions, pseudouridine (Ψ), impacts using...
Protein output from synonymous codons is thought to be equivalent if appropriate tRNAs are sufficiently abundant. Here we show that mRNAs encoding iterated lysine codons, AAA or AAG, differentially impact protein synthesis: insertion of into an ORF diminishes expression more than AAG codons. Kinetic studies in E. coli reveal differential production results pausing on consecutive AAA-lysines followed by ribosome sliding homopolymeric A sequence. Translation a cell-free system demonstrates...
Conserved poly(A) tracks in coding regions are attenuators of translation.
Post-transcriptional modifications to messenger RNAs (mRNAs) have the potential alter biological function of this important class biomolecules. The study mRNA is a rapidly emerging field, and full complement chemical in mRNAs not yet established. We sought identify quantify present yeast using an ultra-high performance liquid chromatography tandem mass spectrometry method detect 40 nucleoside variations parallel. observe six modified nucleosides with high confidence highly purified samples...
While the centrality of posttranscriptional modifications to RNA biology has long been acknowledged, function vast majority modified sites remains be discovered. Illustrative this, there is not yet a discrete biological role assigned for one most highly conserved modifications, 5-methyluridine at position 54 in tRNAs (m
Significance Pseudouridine is among the most-abundant RNA modifications. We present a framework for conceptualizing how eukaryotic pseudouridine synthases select their substrates. This work reveals structure of yeast synthase 7 (Pus7) and presents cell-based biochemical investigations enzyme binding activity. demonstrate that Pus7 interacts promiscuously with RNAs containing UG U AR sequences. Our observations raise question why these enzymes only modify <5% sequences in transcriptome,...
Abstract CGG repeat expansions in the FMR1 5’UTR cause neurodegenerative disease Fragile X-associated tremor/ataxia syndrome (FXTAS). These repeats form stable RNA secondary structures that support aberrant translation absence of an AUG start codon (RAN translation), producing aggregate-prone peptides accumulate within intranuclear neuronal inclusions and contribute to neurotoxicity. Here, we show most abundant RAN product, FMRpolyG, is markedly less toxic when generated from a construct...
The ribosome utilizes hydrogen bonding between mRNA codons and aminoacyl-tRNAs to ensure rapid accurate protein production. Chemical modification of nucleobases can adjust the strength pattern this alter synthesis. We investigate how N1-methylpseudouridine (m
During systemic RNA interference (RNAi) in Caenorhabditis elegans, spreads across different cells and tissues a process that requires the deficient-1 (sid-1) gene, which encodes an integral membrane protein. SID-1 acts cell-autonomously is required for cellular import of interfering RNAs. Heterologous expression Drosophila Schneider 2 enables passive uptake dsRNA subsequent soaking RNAi. Previous studies have suggested may serve as channel, but its precise molecular role remains unclear. To...
Four new mRNA modifications were detected in S. cerevisiae by integrating an improved LC-MS/MS approach with enhanced purification and validation process. Codons containing these further identified to impede translation.
Translation termination is promoted by class 1 and 2 release factors in all domains of life. While the role bacterial factors, RF1 RF2, translation well understood, precise contribution factor, RF3, to this process remains less clear. Here, we use a combination binding assays pre-steady state kinetics provide kinetic thermodynamic framework for understanding translational GTPase RF3 termination. First, find that GDP GTP have similar affinities that, on average, t 1/2 nucleotide dissociation...
siRNA therapeutics provide a selective and powerful approach to reduce the expression of disease-causing genes. For regulatory approval, these modalities require sequence confirmation which is typically achieved by intact tandem mass spectrometry sequencing. However, this process produces highly complex spectra are difficult interpret results in less than full coverage. We sought develop bottom-up sequencing platform ease data analysis Analogous proteomics, requires chemical or enzymatic...
Among RNAs, transfer RNAs (tRNAs) contain the widest variety of abundant posttranscriptional chemical modifications. These modifications are crucial for tRNAs to participate in protein synthesis, promoting proper tRNA structure and aminoacylation, facilitating anticodon:codon recognition, ensuring reading frame maintenance ribosome. While were long thought be stoichiometric, it is becoming increasingly apparent that these can change dynamically response cellular environment. The ability...
Abstract Transfer RNAs (tRNAs) contain dozens of chemical modifications. These modifications are critical for maintaining tRNA tertiary structure and optimizing protein synthesis. Here we advance the use Nanopore direct RNA-sequencing (DRS) to investigate synergy between that known stabilize structure. We sequenced 42 cytosolic isoacceptors from wild-type yeast five tRNA-modifying enzyme knockout mutants. data permitted comprehensive analysis three neighboring conserved in T-loops:...
Functionally critical metals interact with RNA through complex coordination schemes that are currently difficult to visualize at the atomic level under solution conditions. Here, we report a new approach combines NMR and XAS resolve characterize metal binding in most highly conserved P4 helix of ribonuclease P (RNase P), ribonucleoprotein catalyzes divalent ion-dependent maturation 5' end precursor tRNA. Extended X-ray absorption fine structure (EXAFS) spectroscopy reveals Zn(2+) bound mimic...
Type-III CRISPR-Cas systems have recently been adopted for sequence-specific detection of SARS-CoV-2. Here, we repurpose the type III-A CRISPR complex from Thermus thermophilus (TtCsm) programmable capture and concentration specific RNAs mixtures. The target bound TtCsm generates two cyclic oligoadenylates (i.e., cA
Students enroll in biochemistry courses for many reasons, whether it be to build a strong foundation content health science-related careers or better understand the world around them. Learning is enriched when students can identify relevance of content, such as through connecting course authentic applications. One way that make these connections by practicing science communication, an increasingly important skill master. Drawing upon advantages writing, we designed assignment tasked with...
The epigenetic landscape of a cell frequently changes in response to fluctuations nutrient levels, but the mechanistic link is not well understood. In fission yeast, JmjC domain protein Epe1 critical for maintaining heterochromatin landscape. While loss results expansion, overexpression leads defective heterochromatin. Through genetic screen, we found that mutations genes cAMP signaling pathway suppress defects associated with overexpression. We further demonstrated activation Pka1,...
Ribosome speed is dictated by multiple factors including substrate availability, cellular conditions, and product (peptide) formation. Translation slows during the synthesis of cationic peptide sequences, potentially influencing expression thousands proteins. Available evidence suggests that ionic interactions between positively charged nascent peptides negatively ribosome exit tunnel impede translation. However, this hypothesis was difficult to test directly because inability decouple...