A5030932656- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- RNA Interference and Gene Delivery
- Infective Endocarditis Diagnosis and Management
- Genomics and Phylogenetic Studies
- MicroRNA in disease regulation
- HIV Research and Treatment
- Mitochondrial Function and Pathology
- HIV/AIDS drug development and treatment
- Fungal and yeast genetics research
- DNA and Nucleic Acid Chemistry
- Advanced biosensing and bioanalysis techniques
- Chromosomal and Genetic Variations
- Metabolism and Genetic Disorders
- Transplantation: Methods and Outcomes
- Cancer, Lipids, and Metabolism
- interferon and immune responses
- Hepatitis C virus research
- DNA Repair Mechanisms
- CRISPR and Genetic Engineering
- Angiogenesis and VEGF in Cancer
- Plant and Fungal Interactions Research
- Circular RNAs in diseases
Thomas Jefferson University
2015-2024
Computational Physics (United States)
2015-2024
University of Minnesota
2015
Sidney Kimmel Cancer Center
2015
Philadelphia University
2015
The University of Tokyo
2009-2013
Significance Although transfer RNAs (tRNAs) are best known as adapter molecules essential for translation, recent biochemical and computational evidence has led to a previously unexpected conceptual consensus that tRNAs not always end products but can further serve source of small functional RNAs. Here we report novel type tRNA-derived RNA, termed SHOT-RNAs, specifically abundantly expressed in sex hormone-dependent breast prostate cancers. SHOT-RNAs produced from aminoacylated mature by...
MINTbase is a repository that comprises nuclear and mitochondrial tRNA-derived fragments ('tRFs') found in multiple human tissues. The original version of comprised tRFs obtained from 768 transcriptomic datasets. We used our deterministic exhaustive tRF mining pipeline to process all Cancer Genome Atlas datasets (TCGA). identified 23 413 with abundance ≥ 1.0 reads-per-million (RPM). To facilitate further studies by the community, we just released 2.0 contains information about 26 531...
Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology molecular mechanisms underlying them, an efficient sequencing method is required. However, rigid structure has been presenting a challenge to development such methods. We report Y-shaped Adapter-ligated MAture TRNA (YAMAT-seq), convenient for high-throughput mature tRNAs. YAMAT-seq...
Toll-like receptors (TLRs) play a crucial role in the innate immune response. Although endosomal TLR7 recognizes single-stranded RNAs, their endogenous RNA ligands have not been fully explored. Here, we report 5′-tRNA half molecules as abundant activators of TLR7. Mycobacterial infection and accompanying surface TLR activation up-regulate expression human monocyte-derived macrophages (HMDMs). The accumulation halves also occur HMDM-secreted extracellular vehicles (EVs); abundance EV-5′-tRNA...
Mycobacterium tuberculosis (Mtb) infection is among the world's deadliest infectious diseases. Developing effective treatments and biomarkers for requires a deeper understanding of its pathobiology host responses. Here, we report comprehensive characterization circulating short non-coding RNAs (sncRNAs) in plasma samples from Mtb-infected patients. We achieved this by pre-treating with T4 polynucleotide kinase to convert all RNA ends those compatible sncRNA sequencing. discovered global...
Chronic obstructive pulmonary disease (COPD) is the most prevalent lung disease, and macrophages play a central role in inflammatory response COPD. We here report comprehensive characterization of circulating short non-coding RNAs (sncRNAs) plasma from patients with While sncRNAs are increasingly recognized for their regulatory roles biomarker potential various diseases, conventional RNA sequencing (RNA-seq) method cannot fully capture these due to heterogeneous terminal structures. By...
Abstract Great effort has been devoted to discovering the basis of A3G-Vif interaction, key event HIV’s counteraction mechanism evade antiviral innate immune response. Here we show reconstitution complex and subsequent A3G ubiquitination in vitro report cryo-EM structure at 2.8 Å resolution using solubility-enhanced variants Vif. We present an atomic model interface, which assembles via known amino acid determinants. This assembly is not achieved by protein-protein interaction alone, but...
We report a Caucasian boy with intractable epilepsy and global developmental delay. Whole-exome sequencing identified the likely genetic etiology as novel p.K212E mutation in X-linked gene HSD17B10 for mitochondrial short-chain dehydrogenase/reductase SDR5C1. Mutations cause HSD10 disease, traditionally classified metabolic disorder due to role of SDR5C1 fatty amino acid metabolism. However, is also an essential subunit human RNase P, enzyme responsible 5′-processing methylation purine-9...
RNA molecules generated by ribonuclease cleavage sometimes harbor a 2′,3′-cyclic phosphate (cP) at their 3′-ends. Those cP-containing RNAs (cP-RNAs) form hidden layer of transcriptome because standard RNA-seq cannot capture them as result cP's prevention an adapter ligation reaction. Here we provide genome-wide analyses short cP-RNA across multiple mouse tissues. Using cP-RNA-seq that can exclusively sequence cP-RNAs, identified numerous novel species which are mainly derived from...
Transfer RNAs (tRNAs) are fundamental adapter components of translational machinery. tRNAs can further serve as a source tRNA-derived noncoding that play important roles in various biological processes beyond translation. Among all species tRNAs, tRNA HisGUG has been known to uniquely contain an additional guanosine residue at the −1 position (G ) its 5′-end. To analyze this nucleotide detail, we developed TaqMan qRT-PCR method distinctively quantify human mature cytoplasmic containing G , U...
Eukaryotic cells equip robust systems to respond stress conditions. In stressed mammalian cells, angiogenin endoribonuclease cleaves anticodon-loops of tRNAs generate tRNA halves termed tRNA-derived stress-induced RNAs (tiRNAs), which promote granule formation and regulate translation. The 5'-tiRNAs (5'-tRNA halves) contain a 2',3'-cyclic phosphate (cP) thus belong cP-containing (cP-RNAs). cP-RNAs form hidden layer the transcriptome because standard RNA-seq cannot amplify sequence them. this...
Transfer RNAs (tRNAs) play a central role in translation and also recently appear to have variety of other functions biological processes beyond translation. Here we report the development Four-Leaf clover qRT-PCR (FL-PCR), convenient PCR-based method, which can specifically quantify individual mature tRNA species. In FL-PCR, T4 RNA ligase 2 ligates stem-loop adapter tRNAs but not precursor or fragments. Subsequent TaqMan amplifies only unmodified regions tRNA-adapter ligation products;...
Abstract Canonical RNA processing in mammalian mitochondria is defined by tRNAs acting as recognition sites for nucleases to release flanking transcripts. The relevant factors, their structures, and mechanism are well described, but not all mitochondrial transcripts punctuated tRNAs, mode of has remained unsolved. Using Drosophila mouse models, we demonstrate that non-canonical results the formation 3′ phosphates, phosphatase activity carbon catabolite repressor 4 domain-containing family...
Abstract Piwi proteins and their bound Piwi-interacting RNAs (piRNAs) are predominantly expressed in the germline play crucial roles development by silencing transposons other targets. Bombyx mori BmN4 cells culturable germ that equip piRNA pathway. Because of scarcity piRNA-expressing cells, being utilized for analyses biogenesis. We here report biogenesis is regulated cell density. As density increased, abundance factors was commonly upregulated, resulting an increased number perinuclear...
In animal germlines, PIWI proteins and the associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons. Here we report extensive sequence quantitative correlations between 2',3'-cyclic phosphate-containing (cP-RNAs), identified using cP-RNA-seq, piRNAs in Bombyx germ cell line mouse testes. The cP-RNAs containing 5'-phosphate (P-cP-RNAs) P-cP-RNA-seq harbor highly consistent 5'-end positions as are loaded onto protein, suggesting their direct utilization piRNA...
Angiogenin (Ang), an endoribonuclease belonging to the RNase A superfamily, cleaves anticodon-loops of tRNAs produce tRNA half molecules. Although previous studies have demonstrated involvement Ang in pathobiology neurodegenerative disorders, characterization Ang-generated halves neuronal cells remains limited. This is partly due technical limitations standard RNA-seq methods, which cannot capture RNAs containing a 2',3'-cyclic phosphate (cP). In this report, we established treatment model...
Post-transcriptional non-template additions of nucleotides to 3'-ends RNAs play important roles in the stability and function RNA molecules. Although tRNA nucleotidyltransferase (CCA-adding enzyme) is known add CCA trinucleotides tRNAs, whether other species can be endogenous substrates CCA-adding enzyme has not been widely explored yet. Herein, we used YAMAT-seq identify non-tRNA enzyme. captures that form secondary structures with 4-nt protruding sequence 5'-NCCA-3', which hallmark...
Abstract Colicin D is a plasmid‐encoded antibacterial protein that specifically cleaves the anticodon loops of four Escherichia coli tRNA Arg species. Here, we report catalytic domain colicin D, which expressed in Saccharomyces cerevisiae , impairs cell growth by cleaving specific tRNAs. DNA microarray analysis revealed mating‐related genes were upregulated, while involved range metabolic processes downregulated, thereby impairing growth. The pheromone‐signalling pathway was activated only α...