A5004461127- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- MicroRNA in disease regulation
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Vibrio bacteria research studies
- Ubiquitin and proteasome pathways
- Biochemical and Molecular Research
- Peptidase Inhibition and Analysis
- Plant Virus Research Studies
- Chromosomal and Genetic Variations
- interferon and immune responses
- Cancer-related molecular mechanisms research
- Enzyme Structure and Function
- RNA Interference and Gene Delivery
- Evolution and Genetic Dynamics
- T-cell and B-cell Immunology
- Glycosylation and Glycoproteins Research
- Advanced biosensing and bioanalysis techniques
- Aquaculture disease management and microbiota
- Immune Cell Function and Interaction
National Center for Biotechnology Information
2016-2025
National Institutes of Health
2016-2025
United States National Library of Medicine
2007-2023
RIKEN Center for Integrative Medical Sciences
2009-2021
NTL Institute for Applied Behavioral Science
2017
RIKEN
2011
Boston University
2006-2008
Animal microRNA sequences are subject to 3′ nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation miRNA is globally present conserved across Drosophila vertebrates. To better understand function, after knockdown nucleotidyltransferase enzymes. The PAPD4 adenylates a wide range loci, but does not appear affect stability on genome-wide scale. Adenine addition appears reduce effectiveness targeting mRNA transcripts while...
While several studies have focused on the relationship between individual miRNA loci or classes of small RNA with human Argonaute (AGO) proteins, a comprehensive, global analysis content associating different AGO proteins has yet to be performed. We compared deep sequenced extracted from immunoprecipitation experiments AGO1, AGO2, and AGO3 proteins. Consistent previous observations, sequence tags derived globally associate in approximately equivalent amounts AGO3. Exceptions include miR-182,...
Abstract Background The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks large part to the advances comparative genomics. Typically, evolve rapidly hampering identification these proteins by sequence analysis. Here we analyze an unexpectedly widespread superfamily toxin domains most which possess RNase activity. Results HEPN is comprised α-helical were first identified as being associated with DNA...
Cyclic di- and linear oligo-nucleotide signals activate defenses against invasive nucleic acids in animal immunity; however, their evolutionary antecedents are poorly understood. Using comparative genomics, sequence structure analysis, we uncovered a vast network of systems defined by conserved prokaryotic gene-neighborhoods, which encode enzymes generating such nucleotides or alternatively processing them to yield potential signaling molecules. The nucleotide-generating include several...
Ubiquitin (Ub)-mediated signaling is one of the hallmarks all eukaryotes. Prokaryotic homologs Ub (ThiS and MoaD) E1 ligases have been studied in relation to sulfur incorporation reactions thiamine molybdenum/tungsten cofactor biosynthesis. However, there no evidence for entire protein modification systems with Ub-like proteins deconjugation by deubiquitinating enzymes prokaryotes. Hence, evolutionary assembly eukaryotic Ub-signaling apparatus remains unclear.We systematically analyzed...
Next-generation sequencing experiments have shown that microRNAs (miRNAs) are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found mature miR-21, the most widely researched miRNA because of its importance human disease, produced two prevalent isomiR forms differ by 1 nt at their 3' end, and moreover end miR-21 posttranscriptionally adenylated noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase expression level, suggesting...
Discovery of the TET/JBP family dioxygenases that modify bases in DNA has sparked considerable interest novel base modifications and their biological roles. Using sensitive sequence structure analyses combined with contextual information from comparative genomics, we computationally characterize over 12 biochemical systems for modifications. We predict previously unidentified enzymes, such as kinetoplastid J-base generating glycosyltransferase (and its homolog GREB1), catalytic specificity...
Naturally occurring regulatory T (Treg) cells, which specifically express the transcription factor forkhead box P3 (Foxp3), are engaged in maintenance of immunological self-tolerance and homeostasis. By transcriptional start site cluster analysis, we assessed here how genome-wide patterns DNA methylation or Foxp3 binding sites were associated with Treg-specific gene expression. We found that hypomethylated regions closely Treg up-regulated clusters, whereas had no significant correlation...
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects biology. By performing a comparative genomics analysis 224 jumbo phages, we suggest an objective inclusion criterion based on distributions present synthetic overview manifold adaptations across major biological systems. means clustering principal component the phyletic patterns conserved genes, all known can be classified into three higher-order groups, which include both myoviral...
Recent studies have shown that the ubiquitin system had its origins in ancient cofactor/amino acid biosynthesis pathways. Preliminary also indicated conjugation systems for other peptide tags on proteins, such as pupylation, evolutionary links to Following up these observations, we systematically investigated non-ribosomal amidoligases of ATP-grasp, glutamine synthetase-like and acetyltransferase folds by classifying known members identifying novel versions. We then established their...
Spliceostatin A (SSA) is a methyl ketal derivative of FR901464, potent antitumor compound isolated from culture broth Pseudomonas sp . no. 2663. These compounds selectively bind to the essential spliceosome component SF3b, subcomplex U2 snRNP, inhibit pre-mRNA splicing. However, mechanism SSA's activity unknown. It noteworthy that SSA causes accumulation truncated form CDK inhibitor protein p27 translated CDKN1B pre-mRNA, which involved in SSA-induced cell-cycle arrest. it still unclear...
Both prokaryotic and eukaryotic immune systems face the dangers of premature activation effectors degradation self-molecules in absence an invader. To mitigate this, they have evolved threshold-setting regulatory mechanisms for triggering only upon detection a sufficiently strong invader signal. This work defines general templates such regulation effector-based systems. Using we identify several previously uncharacterized that accomplish downstream effector deployment by using nucleotide,...