Publications by authors named "Emily Zahn"
Histone post-translational modifications (PTMs) regulate gene expression patterns through epigenetic mechanisms. The 5 histone proteins (H1, H2A, H2B, H3, and H4) are extensively modified, with over 75 distinct modification types spanning more than 200 sites. Despite strong advances in mass spectrometry-based approaches, identification and quantification of modified histone peptides remains challenging due to factors such as isobaric peptides, pseudo-isobaric PTMs, and low stoichiometry of certain marks.
View Article and Find Full Text PDFReversible modification of the histone H3 N-terminal tail is critical in regulating the chromatin structure, gene expression, and cell states, while its dysregulation contributes to disease pathogenesis. Understanding the crosstalk between H3 tail modifications in nucleosomes constitutes a central challenge in epigenetics. Here, we describe an engineered sortase transpeptidase, cW11, that displays highly favorable properties for introducing scarless H3 tails onto nucleosomes.
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- Reversible modifications of the histone H3 N-terminal tail play a key role in regulating chromatin structure, gene expression, and cell states, with their dysregulation linked to diseases.
- The engineered sortase transpeptidase cW11 allows for efficient and seamless introduction of modified H3 tails onto nucleosomes, facilitating research on the effects of these modifications.
- cW11 enables advanced proteomics techniques for studying histone H3 modification interactions after treatments, providing valuable insights for epigenetics research and potential therapeutic applications.
Dysregulated transcription due to disruption in histone lysine methylation dynamics is an established contributor to tumorigenesis. However, whether analogous pathologic epigenetic mechanisms act directly on the ribosome to advance oncogenesis is unclear. Here we find that trimethylation of the core ribosomal protein L40 (rpL40) at lysine 22 (rpL40K22me3) by the lysine methyltransferase SMYD5 regulates mRNA translation output to promote malignant progression of gastric adenocarcinoma (GAC) with lethal peritoneal ascites.
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- Protein arginylation is a crucial posttranslational modification done by the enzyme ATE1, which involves adding an arginine to proteins, making it hard to distinguish from normal arginine present in proteins.
- Researchers introduced a new method called activity-based arginylation profiling (ABAP) that uses isotopic labeling to identify arginylation in various biological samples without interference from translational activities.
- ABAP successfully identified 229 unique arginylation sites in human proteins and can be applied to different samples, helping advance the understanding of this complex protein modification's biological roles.
The interest in MS-based analysis of modified nucleic acids is increasing due to the application of nucleic acids in therapeutics. However, there are few available integrated platforms for characterizing nucleic acid modifications. Herein, we report a general mass spectrometry-based SWATH platform to identify and quantify both RNA and DNA modifications, which we call SWATH analysis of modified nucleic acids (SWAMNA).
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- SPINDLY (SPY) is a newly discovered nucleocytoplasmic protein O-fucosyltransferase (POFUT) in Arabidopsis thaliana that plays a crucial role in various developmental processes.
- The structure of SPY, determined through cryo-electron microscopy, shows it uniquely binds GDP-fucose instead of the typical UDP-GlcNAc, and it forms an antiparallel dimer unlike human counterparts.
- The N-terminal peptide of SPY contains self-fucosylation sites that inhibit its activity, while specific regions (TPRs 1-5) regulate its function by affecting how it interacts with protein substrates.
SPINDLY (SPY) is a novel nucleocytoplasmic protein O-fucosyltransferase that regulates target protein activity or stability via O-fucosylation of specific Ser/Thr residues. Previous genetic studies indicate that AtSPY regulates plant development during vegetative and reproductive growth by modulating gibberellin and cytokinin responses. AtSPY also regulates the circadian clock and plant responses to biotic and abiotic stresses.
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