A5031928215- RNA Research and Splicing
- RNA modifications and cancer
- Fungal and yeast genetics research
- RNA and protein synthesis mechanisms
- HIV Research and Treatment
- RNA regulation and disease
- Endoplasmic Reticulum Stress and Disease
- Microbial Metabolic Engineering and Bioproduction
- Cancer-related molecular mechanisms research
- Bioinformatics and Genomic Networks
- Polyamine Metabolism and Applications
- RNA Interference and Gene Delivery
- Genetics, Aging, and Longevity in Model Organisms
- Fungal Infections and Studies
- Antifungal resistance and susceptibility
- Genomics and Phylogenetic Studies
- Biofuel production and bioconversion
University of Chicago
2018-2020
Yale University
2014-2016
University of Michigan
2010-2013
Michigan United
2011
Pseudouridine (Ψ) is the most abundant RNA modification in cellular present tRNA/rRNA/snRNA and also mRNA long noncoding (lncRNA). Elucidation of Ψ function mRNA/lncRNA requires mapping quantitative assessment its fraction at single-base resolution. The widely used method for relies on reaction with N -Cyclohexyl- ′-(2-morpholinoethyl)carbodiimide (CMC), forming an adduct base that detectable by reverse transcription (RT) stops. However, this has not produced consistent maps mRNAs;...
N6-methyladenosine (m6A) is the most abundant HIV RNA modification but interplay between m6A reader protein YTHDF3 and replication not well understood. We found that knockout of in human CD4+ T-cells increases infection supporting role as a restriction factor. Overexpression producer cells reduces infectivity newly produced viruses. proteins are incorporated into particles nucleocapsid-dependent manner permitting to limit new target cell at step reverse transcription. Importantly, protease...
Advances in high-throughput sequencing have facilitated remarkable insights into the diversity and functioning of naturally occurring microbes; however, current strategies are insufficient to reveal physiological states microbial communities associated with protein translation dynamics. Transfer RNAs (tRNAs) core components synthesis machinery, present all living cells, phylogenetically tractable, which make them ideal targets gain environmental microbes. Here we report a direct approach,...
All retroviruses package cellular RNAs into virions. Studies of murine leukemia virus (MLV) revealed that the major host cell encapsidated by this simple retrovirus were LTR retrotransposons and noncoding (ncRNAs). Several classes ncRNAs appeared to be packaged MLV shortly after synthesis, as precursors tRNAs, small nuclear RNAs, nucleolar all enriched in To determine extent which human immunodeficiency (HIV-1) packages similar we used high-throughput sequencing characterize within...
The morphogenetic transition between yeast and filamentous forms of the human fungal pathogen Candida albicans is regulated by a variety signaling pathways. How these pathways interact to orchestrate morphogenesis, however, has not been as well characterized. To address this question identify genes that with Regulation Ace2 Morphogenesis (RAM) pathway during filamentation, we report first large-scale genetic interaction screen in C. albicans. Our strategy for was based on concept complex...
Abstract The budding yeast Saccharomyces cerevisiae can respond to nutritional and environmental stress by implementing a morphogenetic program wherein cells elongate interconnect, forming pseudohyphal filaments. This growth transition has been studied extensively as model signaling system with similarity processes of hyphal development that are linked virulence in related fungal pathogens. Classic studies have identified core modules yeast; however, the scope regulatory networks control...
Although all retroviruses recruit host cell RNAs into virions, both the spectrum of encapsidated and mechanisms by which they are recruited remain largely unknown. Here, we used high-throughput sequencing to obtain a comprehensive description packaged model retrovirus, murine leukemia virus. The major noncoding (ncRNAs) members VL30 class endogenous retroviruses. Remarkably, although Moloney virus (MLV) assembles in cytoplasm, precursors specific tRNAs, small nuclear (snRNAs), nucleolar...
Over 130 modifications have been identified in cellular RNAs, which play critical roles many processes, from modulating RNA stability to altering translation efficiency. One such modification, 5-methylcytosine, is relatively abundant mammalian mRNAs, but its precise location and function are not well understood. In this study, we unexpectedly high levels of m 5 C the murine leukemia virus RNA, precisely mapped location, showed that ALYREF, a reader protein specifically recognizes C,...
The abundant RNA modification pseudouridine (Ψ) has been mapped transcriptome-wide by chemically modifying pseudouridines with carbodiimide and detecting the resulting reverse transcription stops in high-throughput sequencing. However, these methods have limited sensitivity specificity, part due to use of stops. We sought mutations rather than just sequencing data identify sites. Here, we conditions that allow read-through carbodiimide-modified (CMC-Ψ), show carbodiimide-treated human...
Yeast filamentous growth is a stress response to conditions of nitrogen deprivation, wherein yeast colonies form pseudohyphal filaments elongated and connected cells. As proteins mediating adhesion transport are required for this transition, we expect that the protein complement at cell periphery plays critical tightly regulated role in filamentation. To identify differentially abundant during growth, generated quantitative proteomic profiles plasma membrane preparations under vegetative By...