A5103219999- MicroRNA in disease regulation
- Circular RNAs in diseases
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Viral Infectious Diseases and Gene Expression in Insects
- Invertebrate Immune Response Mechanisms
- CRISPR and Genetic Engineering
- Plant Molecular Biology Research
- Research in Cotton Cultivation
- RNA Interference and Gene Delivery
- Aquaculture Nutrition and Growth
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- DNA Repair Mechanisms
- Microfluidic and Bio-sensing Technologies
- Plant Virus Research Studies
- Membrane Separation Technologies
- RNA regulation and disease
- Bone Metabolism and Diseases
- Silk-based biomaterials and applications
University of Washington
2017-2024
Whitehead Institute for Biomedical Research
2014-2018
Howard Hughes Medical Institute
2014-2018
Massachusetts Institute of Technology
2014-2017
The University of Texas at Austin
2009
Abstract Background The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression. However, the global properties are not well understood. Results We developed a computational pipeline identify and quantify their relative abundance from RNA-seq data. Applying this large set non-poly(A)-selected data ENCODE project, we annotated 7,112 human were estimated comprise at...
Expression changes of competing endogenous RNAs (ceRNAs) have been proposed to influence microRNA (miRNA) activity and thereby regulate other transcripts containing miRNA-binding sites. Here, we find that although miRNA levels define the extent repression, they little effect on magnitude ceRNA expression change required observe derepression. Canonical 6-nt sites, which typically mediate modest can nonetheless compete for binding, with potency ∼20% observed canonical 8-nt In aggregate,...
Algorithms that accurately predict gene structure from primary sequence alone were transformative for annotating the human genome. Can we also expression levels of genes based solely on genome sequence? Here, sought to apply deep convolutional neural networks toward goal. Surprisingly, a model includes only promoter sequences and features associated with mRNA stability explains 59% 71% variation in steady-state mouse, respectively. This model, termed Xpresso, more than doubles accuracy...
Non-homologous end-joining (NHEJ) plays an important role in double-strand break (DSB) repair of DNA. Recent studies have shown that the error patterns NHEJ are strongly biased by sequence context, but these were based on relatively few templates. To investigate this more thoroughly, we systematically profiled ∼1.16 million independent mutational events resulting from CRISPR/Cas9-mediated cleavage and NHEJ-mediated DSB 6872 synthetic target sequences, introduced into a human cell line via...
MicroRNAs (miRNAs) are short regulatory RNAs that derive from hairpin precursors. Important for understanding the functional roles of miRNAs is ability to predict messenger RNA (mRNA) targets most responsive each miRNA. Progress towards developing quantitative models miRNA targeting in Drosophila and other invertebrate species has lagged behind mammals due paucity datasets measuring effects on mRNA levels. We acquired suitable study Drosophila. Analyses these data expanded types sites known...
The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression. However, the global properties are not well understood. We developed a computational pipeline identify and quantify their relative abundance from RNA-seq data. Applying this large set non-poly(A)-selected data ENCODE project, we annotated 7,112 human were estimated comprise at least 10% transcripts...
Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction live imaging a biological sample within timeframe interest. Here we demonstrate an alternative paradigm in which such activities stably recorded to genome. Enhancer-driven genomic recording transcriptional multiplex (ENGRAM) is based on signal-dependent production prime editing guide RNAs mediate insertion signal-specific barcodes (symbols) into...
Significance The vertebral column provides essential structural and protective functions. total number of elements their specific morphologies are remarkably reproducible within a given species, yet can be tailored to the requirements separate vertebrate species. Major genetic determinants driving formation known, but how they regulated achieve highly structure remains fully elucidated. In this report, we show that miR-196 family microRNAs in defining correct identity mouse. We reveal...
Rational design and robust formulation processes are critical for optimal delivery of mRNA by lipid nanoparticles (LNPs). Varying degrees heterogeneity in mRNA-LNPs can affect their biophysical functional properties. Given the profound complexity mRNA-LNPs, it is to develop comprehensive orthogonal analytical techniques a better understanding these formulations. To this end, we developed ultracentrifugation method density-based separation subpopulations mRNA-LNPs. Four LNP formulations...
SUMMARY Algorithms that accurately predict gene structure from primary sequence alone were transformative for annotating the human genome. Can we also expression levels of genes based solely on genome sequence? Here sought to apply deep convolutional neural networks towards this goal. Surprisingly, a model includes only promoter sequences and features associated with mRNA stability explains 59% 71% variation in steady-state mouse, respectively. This model, which call Xpresso, more than...
Abstract Non-homologous end-joining (NHEJ) plays an important role in double-strand break (DSB) repair of DNA. Recent studies have shown that the error patterns NHEJ are strongly biased by sequence context, but these were based on relatively few templates. To investigate this more thoroughly, we systematically profiled ∼1.16 million independent mutational events resulting from CRISPR/Cas9-mediated cleavage and NHEJ-mediated DSB 6,872 synthetic target sequences, introduced into a human cell...
ABSTRACT Important for understanding the regulatory roles of miRNAs is ability to predict mRNA targets most responsive each miRNA. Here, we acquired datasets needed quantitative study microRNA targeting in Drosophila. Analyses these data expanded types sites known be effective flies, regions with detectable include 5′ UTRs, and identified features site context that correlate efficacy. Updated evolutionary analyses evaluated probability conserved predicted indicated more than a third...