A5009185654- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- RNA Interference and Gene Delivery
- MicroRNA in disease regulation
- Advanced biosensing and bioanalysis techniques
- Resilience and Mental Health
- Click Chemistry and Applications
- CRISPR and Genetic Engineering
- HVDC Systems and Fault Protection
- Fungal and yeast genetics research
- Cancer-related molecular mechanisms research
- Microbial Metabolic Engineering and Bioproduction
- Endoplasmic Reticulum Stress and Disease
Eclipse Bioinnovations (United States)
2022
University of California, San Diego
2019-2021
University of Michigan
2014-2020
Washtenaw Community College
2016-2020
Ann Arbor Center for Independent Living
2016-2020
Sonoma State University
2012
Direct RNA sequencing holds great promise for the de novo identification of modifications at single-coordinate resolution; however, interpretation raw output to discover modified bases remains a challenge. Using Oxford Nanopore's direct technology, we developed random forest classifier trained using experimentally detected N 6 -methyladenosine (m A) sites within DRACH motifs. Our software MINES A Identification Nanopore Sequencing) assigned m methylation status more than 13,000 previously...
Dysregulation of microRNA (miRNA) expression has been linked to many human diseases; however, because the challenges associated with RNA-targeted drug discovery, additional approaches are needed for probing miRNA biology. The emerging regulatory role miRNA-binding proteins in maturation presents such an alternative strategy. Exploiting our laboratory's click chemistry-based high-throughput screening (HTS) technology, catalytic enzyme-linked chemistry assay or cat-ELCCA, we have designed a...
microRNAs (miRNAs) are small gene regulatory RNAs, and their expression has been found to be dysregulated in a number of human diseases. To facilitate the discovery molecules capable selectively modulating activity specific miRNA, we have utilized new high-throughput screening technology targeting Dicer-mediated pre-miRNA maturation. Pilot ~50,000 ~33,000 natural product extract libraries against pre-miR-21 processing indicated potential our assay for this goal, yielding campaign Z′ factor...
Transcription and translation are intertwined processes in which mRNA isoforms crucial intermediaries. However, methodological limitations analyzing at the isoform level have left gaps our understanding of critical biological processes. To address these gaps, we developed an integrated computational experimental framework called long-read Ribo-STAMP (LR-Ribo-STAMP) that capitalizes on advancements sequencing RNA-base editing–mediated technologies to simultaneously profile transcription both...
Preservation of both the integrity and fluidity biological membranes is a critical cellular homeostatic function. Signaling pathways that govern lipid bilayer have long been known in bacteria, yet no such identified eukaryotes. Here we identify mutants yeast Saccharomyces cerevisiae whose growth differentially influenced by its two principal unsaturated fatty acids, oleic palmitoleic acid. Strains deficient core components cell wall (CWI) pathway, MAP kinase pathway dependent on Pkc1...
MicroRNAs (miRNA) play critical roles in human development and disease. As such, the targeting of miRNAs is considered attractive as a novel therapeutic strategy. A major bottleneck toward this goal, however, has been identification small molecule probes that are specific for select RNAs methods will facilitate such discovery efforts. Using pre-microRNAs proof-of-concept, herein we report conceptually new innovative approach assaying RNA-small interactions. Through platform assay technology,...
A catalytic enzyme-linked click chemistry assay (cat-ELCCA) for Dicer-catalyzed pre-microRNA maturation was optimized to employ inverse-electron demand Diels–Alder (IEDDA) affording high-throughput screening capability.
Abstract Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites RNA-binding proteins (RBPs). Despite improvements in library preparation fragments, enhanced CLIP (eCLIP) protocol requires 4 days hands-on time lacks ability to process several RBPs parallel. We present a new method termed antibody-barcode eCLIP that utilizes DNA-barcoded antibodies proximity ligation DNA oligonucleotides RBP-protected fragments interrogate...
In a high-throughput screening campaign, we recently discovered the rRNA-binding tetracyclines, methacycline and meclocycline, as inhibitors of Dicer-mediated processing microRNAs. Herein, describe our biophysical biochemical characterization these compounds. Interestingly, although direct, albeit weak, binding to pre-microRNA hairpins was observed, inhibitory activity compounds not due RNA binding. Through additional chemical studies, revealed that metal chelation likely plays principle...
Recent efforts in genome-wide sequencing and proteomics have revealed the fundamental roles that RNA-binding proteins (RBPs) play life cycle function of coding non-coding RNAs. While these methodologies provide a systems-level view networking RNA proteins, approaches to enable cellular validation discovered interactions are lacking. Leveraging power bioorthogonal chemistry- split-luciferase-based assay technologies, we devised conceptually new for live-cell detection RNA-protein (RPIs),...
Click chemistry-based assays are a growing class of biochemical assay for facilitating the discovery modulators important biological processes. To date, most have relied on use immobilized biomolecules, which increases cost and decreases throughput because necessary washing steps. overcome these challenges, we developed click chemistry-mediated complementation that retains many advantages previous technology, including catalytic signal amplification robustness applicability to full-length...
Abstract RNA binding proteins (RBPs) are critical regulators of gene expression and processing that required for function. Yet, the dynamics RBP regulation in single cells is unknown. To address this gap understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP-RNA interactions. does not rely on UV-crosslinking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP- cell type-specific RNA-protein...
Abstract Recent efforts in genome-wide sequencing and proteomics have revealed the fundamental roles that RNA-binding proteins (RBPs) play life cycle function of both coding non-coding RNAs. While these methodologies provide a systems-level view networking RNA proteins, approaches to enable cellular validation discovered interactions are lacking. Leveraging power bioorthogonal chemistry- split-luciferase-based assay technologies, we devised conceptually new for live-cell detection...
Abstract UV cross-linking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites RNA-binding proteins (RBPs). Despite improvements in library preparation fragments, current enhanced CLIP (eCLIP) protocol requires 4 days hands-on time lacks ability to process many RBPs parallel. We present a new method termed antibody-barcode eCLIP (ABC) that utilizes DNA-barcoded antibodies proximity ligation DNA oligonucleotides RBP-protected fragments interrogate...