A5005799757- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- RNA modifications and cancer
- Fungal and yeast genetics research
- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- DNA Repair Mechanisms
- Cell Adhesion Molecules Research
- Microgrid Control and Optimization
- Machine Learning in Bioinformatics
- Microbial Metabolic Engineering and Bioproduction
- Plant-Microbe Interactions and Immunity
- Microbial Natural Products and Biosynthesis
- Distributed and Parallel Computing Systems
- Plant Pathogens and Fungal Diseases
University of Cambridge
2010-2022
University of North Carolina at Chapel Hill
2008-2011
Most cellular processes are conducted by multi-protein complexes. However, little is known about how these complexes assembled. In particular, it not if they formed while one or more members of the being translated (cotranslational assembly). We took a genomic approach to address this question, systematically identifying mRNAs associated with specific proteins. sample 31 proteins from Schizosaccharomyces pombe that did contain RNA–binding domains, we found ∼38% copurify encode interacting...
mRNA half-lives are transcript-specific and vary over a range of more than 100-fold in eukaryotic cells. stabilities can be regulated by sequence-specific RNA-binding proteins (RBPs), which bind to regulatory sequence elements modulate the interaction with cellular RNA degradation machinery. However, it is unclear if this kind regulation sufficient explain large stabilities. To address question, we examined transcriptome 74 Schizosaccharomyces pombe strains carrying deletions non-essential...
Stress conditions lead to global and gene-specific changes in RNA translation. Ribosome profiling experiments have identified genome-wide alterations the distribution of ribosomes along mRNAs. However, it is contentious whether these reflect real responses, or they are artefacts caused by use inhibitors translation (notably cycloheximide). To address this issue we performed ribosome with fission yeast Schizosaccharomyces pombe under exponential growth (unstressed) nitrogen starvation...
Eukaryotes respond to amino acid starvation by enhancing the translation of mRNAs encoding b-ZIP family transcription factors ( GCN4 in Saccharomyces cerevisiae and ATF4 mammals), which launch transcriptional programs counter this stress. This pathway involves phosphorylation eIF2 factor Gcn2-protein kinases is regulated upstream ORFs (uORFs) / 5′ leaders. Here, we present evidence that mediate response are not evolutionarily conserved. Although cells fission yeast Schizosaccharomyces pombe...
Heterochromatin is essential for chromosome segregation, gene silencing and genome integrity. The fission yeast Schizosaccharomyces pombe contains heterochromatin at centromeres, subtelomeres, mating type genes, as well small islands of meiotic genes dispersed across the genome. This generated by partially redundant mechanisms, including production interfering RNAs (siRNAs) that are incorporated into RITS protein complex (RNAi-Induced Transcriptional Silencing). assembly requires function...
Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the and/or dynamics of nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed standard reporting results single nucleotide resolution acid experiments, or SNRNASMs. propose schema sharing probing that uses generic...
Most functional RNAs require proteins to facilitate formation of their active structures. In the case yeast bI3 group I intron, splicing requires binding by two proteins, intron-encoded maturase and nuclear encoded Mrs1. Here, we use selective 2′-hydroxyl acylation analyzed primer extension (SHAPE) chemistry coupled with analysis point mutants map long-range interactions in this RNA. This reveals critical features free RNA state. First, catalytic intron is separated from flanking exons via a...
Fungal infections represent a major clinical, agricultural, and food security threat worldwide, which is accentuated due to the difficult treatment of these infections. Microorganisms prolific source antibiotics, current data support that this enormous biosynthetic potential has been scarcely explored.
Proteins play diverse and critical roles in cellular ribonucleoproteins (RNPs) including promoting formation of stabilizing active RNA conformations. Yet, the conformational changes required to convert large RNAs into RNPs have proven difficult characterize fully. Here we use high-resolution approaches monitor both local nucleotide flexibility solvent accessibility for nearly all nucleotides bI3 group I intron RNP four assembly states: free RNA, maturase-bound Mrs1-bound complete...
Most cellular proteins function as part of stable protein complexes. We recently showed that around 38% associate with mRNAs encode interacting proteins, reflecting the cotranslational formation complex between bait and nascent peptides encoded by mRNAs. Here we hypothesise these protein-mRNA associations can be used to predict protein-protein interactions. found fission yeast Exo2 protein, which encodes an exonuclease XRN1 family, coimmunoprecipitates eti1 mRNA, codes for a unknown...
Most large ribozymes require protein cofactors in order to function efficiently. The yeast mitochondrial bI3 group I intron requires two proteins for efficient splicing, Mrs1 and the maturase. has evolved from DNA junction resolvases as an RNA cofactor at least introns; however, binding site mechanism by which facilitates splicing were unknown. Here we use high-throughput structure analysis show that binds a ubiquitous tertiary motif, GNRA tetraloop-receptor interaction, sites RNA. also...
Genome annotation, assisted by computer programs, is one of the great advances in modern biology. Nevertheless, silico identification small and complex coding sequences still challenging. We observed that amino acid inferred from coding—but rarely non-coding—DNA accumulated alignments low-stringency BLAST searches, suggesting this accumulation could be used to highlight regions sequenced DNA. To investigate possibility, we developed a program (AnABlast) generates profiles query using...
Meiosis is the process by which haploid gametes are produced from diploid precursor cells. We used stable isotope labeling amino acids in cell culture (SILAC) to characterize meiotic proteome fission yeast Schizosaccharomyces pombe. compared relative levels of proteins extracted cells harvested around meiosis I with those II, and premeiotic S phase interval between divisions, when absent. Our datasets revealed peptides corresponding short open reading frames (sORFs) that have been previously...
Characterizing the interactions between RNAs and proteins in vivo is key to better understand how organisms regulate gene expression. Here, we describe a robust quantitative protocol measure specific RNA-protein native context using RNA immunoprecipitation (RIP). We provide comprehensive experimental framework detect cotranslational detail analysis of purified by PCR high-throughput sequencing. Although developed fission yeast, it can be readily implemented other yeast species. For complete...