A5049057337- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA regulation and disease
- Cancer-related gene regulation
- Genomics and Chromatin Dynamics
- Fungal and yeast genetics research
- Molecular Biology Techniques and Applications
- RNA Interference and Gene Delivery
- Trace Elements in Health
- Mitochondrial Function and Pathology
- Peptidase Inhibition and Analysis
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Polyamine Metabolism and Applications
- Cellular Mechanics and Interactions
- Viral Infections and Immunology Research
- Cardiomyopathy and Myosin Studies
- Iron Metabolism and Disorders
- Photosynthetic Processes and Mechanisms
- Galectins and Cancer Biology
- HVDC Systems and Fault Protection
- Protein Degradation and Inhibitors
- Nuclear Structure and Function
- Plant Disease Resistance and Genetics
University of California, Los Angeles
2015-2025
UCLA Health
2024
Centre National de la Recherche Scientifique
1993-2007
Joint Genome Institute
2007
Institut de Biologie Physico-Chimique
2007
Sorbonne Université
2007
Duke University
2007
University of Massachusetts Chan Medical School
2007
Purdue University West Lafayette
2004
University of Wisconsin–Madison
2001
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It model system for studying chloroplast-based photosynthesis, as well the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited common ancestor animals, but lost in plants. We sequenced ∼120-megabase nuclear genome performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated...
Copper formulations have been used for decades antimicrobial and antifouling applications. With the development of nanoformulations copper that are more effective than their ionic microsized analogues, a key regulatory question is whether these materials should be treated as new or existing materials. To address this issue, here we compare magnitude mechanisms toxicity series Cu species (at concentration ranging from 2 to 250 μg/mL), including nano Cu, CuO, Cu(OH)2 (CuPro Kocide), micro Cu2+...
Saccharomyces cerevisiae has been used as a model system to investigate the mechanisms of pre-mRNA splicing but only few examples alternative splice site usage have described in this organism. Using RNA-Seq analysis nonsense-mediated mRNA decay (NMD) mutant strains, we show that many S. intron-containing genes exhibit sites, transcripts generated by at these sites are non-functional because they introduce premature termination codons, leading degradation NMD. Analysis mutants combined with...
Specific recognition of double-stranded RNA (dsRNA) by dsRNA-binding domains (dsRBDs) is involved in a large number biological and regulatory processes. Although structures dsRBDs complex with dsRNA have revealed how they can bind to general, these do not explain dsRBD recognize specific RNAs. Rnt1p, member the RNase III family endonucleases, key component Saccharomyces cerevisiae RNA-processing machinery. The Rnt1p has been implicated targeting this endonuclease its substrates, recognizing...
Almost all small eukaryotic RNAs are processed from transiently stabilized 3-extended forms.A key question is how and why such intermediates they can then be to the mature RNA.Here we report that yeast U3 also a precursor.The major forms of (U3-3I -II) lack cap trimethylation present in not associated with nucleolar RNP (snoRNP) proteins bind U3, i.e., Nop1p, Nop56p, Nop58p.Depletion Nop58p leads loss but increases level U3-3I -II, indicating requirement for snoRNP final maturation.Pre-U3...
The splicing of group II introns occurs in two steps involving substrates with different chemical configurations. question whether these are catalyzed by a single or separate active sites is matter debate. Here, certain bases and phosphate oxygen atoms at conserved positions domain V self-splicing intron shown to be required for catalysis both steps. These results show that the catalyzing must, least, share common components, ruling out existence completely distinct introns.
The cellular components required to form the 3′ ends of small nuclear RNAs are unknown. U5 snRNA from Saccharomyces cerevisiae is found in two forms that differ length at their (U5L and U5S). When added a yeast cell free extract, synthetic pre-U5 RNA bearing downstream genomic sequences processed efficiently accurately generate both mature U5. produced vitro by alternative 3′-end processing. A temperature-sensitive mutation RNT1 gene encoding RNase III blocks accumulation U5L vivo. In vitro,...
The nuclear exosome is involved in a large number of RNA processing and surveillance pathways. RNase III cleavage intermediates destined to be 3′-processed or degraded can detected when the Rrp6p subunit absent. Here we show that these degradation are polyadenylated, their polyadenylation dependent on activity Trf4p Trf5p, two variant poly(A) polymerases. Polyadenylation was inhibited absent, reduced various extents absence suggesting polymerases play functionally distinct roles species....
In addition to mitochondrial DNA, double-stranded RNA (mtdsRNA) is exported from mitochondria. However, specific channels for transport have not been demonstrated. Here, we begin characterize channel candidates mtdsRNA export the matrix cytosol. Down-regulation of SUV3 resulted in accumulation mtdsRNAs matrix, whereas down-regulation PNPase Targeting experiments show that functions both intermembrane space and matrix. Strand-specific sequencing confirms origin. Inhibiting or down-regulating...
Splicing of terminal introns is coupled to 3'-end processing by cleavage and polyadenylation (CPA) mRNAs in mammalian genes. Whether this functional coupling universally conserved across eukaryotes unknown. Here we show using long read RNA sequencing S . cerevisiae that splicing inactivation does not result widespread CPA impairment lead global defects. However, 5'-extensions due termination defects from upstream genes inhibition a length-dependent manner. Additionally, for some extended...
Ribonucleases III are double-stranded RNA (dsRNA) endonucleases required for the processing of a large number prokaryotic and eukaryotic transcripts. Although specificity bacterial RNase cleavage relies on antideterminants in dsRNA, molecular basis is unknown. All substrates yeast (Rnt1p) capped by terminal tetraloops showing consensus AGNN located within 13-16 bp to Rnt1p sites. We show that these essential distance tetraloop primary determinant site selection. The presence also enhances...
Bis(peroxo)vanadium(V) complexes are widely investigated as anticancer agents. They exert their antitumor and cyctotoxic effects through inhibition of tyrosine phosphatases DNA cleavage, respectively. The latter process remains poorly understood. mechanism cleavage by NH4[(phen)V(O)(η2-O2)2] (phen = 1,10-phenanthroline) was investigated. Kinetic studies on revealed that the complex is a single-strand nicking agent with no specificity. EPR experiments using 2,2,6,6-tetramethyl-4-piperidone...
H/ACA small nucleolar ribonucleoprotein particles (snoRNPs) are essential for the maturation and pseudouridylation of precursor rRNAs other stable RNAs. Although RNA protein components these RNPs have been identified, mechanisms by which they assembled in vivo poorly understood. Here we show that binding Naf1p, is required snoRNPs stability, associates with polymerase II-associated proteins Spt16p, Tfg1p, Sub1p snoRNP proteins. Chromatin immunoprecipitation experiments Naf1p...
RNA polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p (NNS) pathway is critical for production of stable noncoding RNAs and control pervasive in Saccharomyces cerevisiae To uncover determinants NNS termination, we mapped 3'-ends NNS-terminated transcripts genome-wide. We found that nucleosomes specific DNA-binding proteins, including general regulatory factors (GRFs) Reb1p, Rap1p, Abf1p, Pol III enhance efficiency physically blocking progression. The same DNA-bound...