A5055163675- Genomics and Chromatin Dynamics
- Fungal and yeast genetics research
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- CAR-T cell therapy research
- Cancer-related gene regulation
- Ubiquitin and proteasome pathways
- Epigenetics and DNA Methylation
- DNA Repair Mechanisms
- CRISPR and Genetic Engineering
- Immune Cell Function and Interaction
- Endoplasmic Reticulum Stress and Disease
- Gene Regulatory Network Analysis
- RNA Research and Splicing
- Immunotherapy and Immune Responses
- RNA Interference and Gene Delivery
- Microbial Metabolic Engineering and Bioproduction
- Protein Degradation and Inhibitors
- Protein Structure and Dynamics
- Genetic factors in colorectal cancer
- Advanced biosensing and bioanalysis techniques
- Bacterial Genetics and Biotechnology
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Cellular transport and secretion
GeneTrace Systems (United States)
2023
University of California, San Francisco
2010-2020
Quantitative BioSciences
2020
QB3
2007-2014
TU Dresden
2002-2009
University of California, San Diego
2008
National Cancer Institute
2008
Center for Cancer Research
2008
Howard Hughes Medical Institute
2008
Bulgarian Academy of Sciences
2000-2007
An epistasis map (E-MAP) was constructed in the fission yeast, Schizosaccharomyces pombe, by systematically measuring phenotypes associated with pairs of mutations. This high-density, quantitative genetic interaction focused on various aspects chromosome function, including transcription regulation and DNA repair/replication. The E-MAP uncovered a previously unidentified component RNA interference (RNAi) machinery (rsh1) linked RNAi pathway to several other biological processes. Comparison...
Set3 is one of two proteins in the yeast Saccharomyces cerevisiae that, like Drosophila Trithorax, contains both SET and PHD domains. We found that forms a single complex, Set3C, with Snt1, YIL112w, Sif2, Cpr1, putative histone deacetylases, Hos2 NAD-dependent Hst1. Set3C includes independent deacetylase activities when assayed vitro. Homology searches suggest analog mammalian HDAC3/SMRT complex. represses genes early/middle sporulation program, including key meiotic regulators ime2 ndt80 ....
Analysis of the phosphoproteomes and gene interaction networks divergent yeast species defines relative contribution changes in protein phosphorylation pathways to generation phenotypic diversity.
Existing evidence indicates that SET2, the histone 3 lysine 36 methyltransferase of Saccharomyces cerevisiae, is a transcriptional repressor. Here we show by five main lines SET2 involved in elongation. First, most, if not all, subunits RNAP II holoenzyme co-purify with SET2. Second, all co-purifying subunit, RPO21, was phosphorylated at serines 5 and 2 C-terminal domain (CTD) tail, indicating association specific to either elongating or SSN3 repressed forms (or both) II. Third, CTD RPO21...
Understanding the design logic of living systems requires understanding and comparison proteomes. Proteomes define commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding accuracy proteomic data, several issues need to be resolved before comparative proteomics can fruitful.The Saccharomyces cerevisiae proteome presents highest quality data available. To evaluate these we intensively mapped a environment, termed 'Chromatin Central', which...
Cells are regularly exposed to stress conditions that may lead protein misfolding. To cope with this challenge, molecular chaperones selectively target structurally perturbed proteins for degradation via the ubiquitin-proteasome pathway. In mammals co-chaperone BAG-1 plays an important role in system. has two orthologues, Bag101 and Bag102, fission yeast Schizosaccharomyces pombe. We show both Bag102 interact 26S proteasomes Hsp70. By epistasis mapping we identify a mutant conserved...
Acute myeloid leukemia (AML) is an aggressive disease with a poor prognosis (5-year survival rate of 30.5% in the United States). Designing cell therapies to target AML challenging because no single tumor-associated antigen (TAA) highly expressed on all cancer subpopulations. Furthermore, TAAs are also healthy cells, leading toxicity risk. To address these targeting challenges, we engineer natural killer (NK) cells multi-input gene circuit consisting chimeric receptors (CARs) controlled by...
The proteasome regulates histone lysine methylation and gene transcription, but how it does so is poorly understood. To better understand this process, we used the epistatic miniarray profile (E-MAP) approach to identify factors that genetically interact with proteasomal subunits. In addition members of Set1 complex mediate H3 4 (H3K4me), found deleting CCR4/NOT mRNA processing exhibit synthetic phenotypes when combined mutants. Further biochemical analyses revealed physical associations...
Histone 3 lysine 4 (H3 Lys(4)) methylation in Saccharomyces cerevisiae is mediated by the Set1 complex (Set1C) and dependent upon ubiquitinylation of H2B Rad6. Mutually exclusive H3 at Lys(4) or Lys(9) central to chromatin regulation; however, S. lacks methylation. Furthermore, a different methylase, Set 7/9, has been identified mammals, thereby questioning relevance findings for eukaryotes general. We report that majority Schizosaccharomyces pombe, like cerevisiae, Set1C Rad6-dependent....
Eukaryotic genomes are repetitively packaged into chromatin by nucleosomes, however they regulated the differences between which establish various states. Local cues direct inheritance and propagation of status via self-reinforcing epigenetic mechanisms. Replication-independent histone exchange could potentially perturb if chaperones, such as Swr1C, loaded variants wrong sites. Here we show that in Schizosaccharomyces pombe, like Saccharomyces cerevisiae, Swr1C is required for loading H2A.Z...
We employed a combination of tandem affinity purification and mass spectrometry for deciphering protein complexes the interaction network in budding yeast. 53 genes were epitope-tagged, their partners isolated by two-step immunoaffinity chromatography from whole cell lysates. 38 baits pulled down total 220 partners, which are members 19 functionally distinct complexes. identified four proteins shared between different functionality thus charting segments network. Concordance with results...
The file extension for Dataset S2 was incorrectly listed. correct is .RAR. To open the file, download it and then add .RAR extension, renaming to journal.pbio.1000134.s002.rar.
Ribonucleotide reductase (RNR) and deoxycytidylate deaminase (dCMP deaminase) are pivotal allosteric enzymes required to maintain adequate pools of deoxyribonucleoside triphosphates (dNTPs) for DNA synthesis repair. Whereas RNR inhibition slows replication activates checkpoint responses, the effect dCMP deficiency is largely unknown. Here, we report that deleting Schizosaccharomyces pombe dcd1(+) gene (SPBC2G2.13c) increases dCTP ∼30-fold decreases dTTP ∼4-fold. In contrast robust growth a...