The Experts below are selected from a list of 18330 Experts worldwide ranked by ideXlab platform
Tomozumi Imamichi - One of the best experts on this subject based on the ideXlab platform.
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siRNA containing a unique 5-Nucleotide Motif acts as a quencher of IFI16-mediated innate immune response
Molecular Immunology, 2019Co-Authors: Jun Yang, Xiaojun Hu, Qian Chen, Tomozumi ImamichiAbstract:Abstract We previously reported that some small interfering RNA (siRNA) enhances DNA or DNA virus mediated-interferon (IFN)-λ1(a type III IFN) induction through the crosstalk between retinoic acid-inducible gene I (RIG-I) and interferon gamma-inducible protein 16 (IFI16) signalling pathway. Here we provide further evidence of a new role for siRNA. siRNA containing a 5-Nucleotide (nt) Motif sequence suppresses DNA-mediated not only type III IFNs, but also type I IFNs and inflammatory cytokines. We define that Motif siRNA inhibits the induction when the Motif is located at the 3′ or 5′-terminus of siRNA. Using THP1-Lucia ISG cells with various DNA stimulants, we reveal that Motif siRNA inhibits DNA or DNA virus but not RNA virus-mediated signalling. Motif siRNA specifically interrupts IFI16 but not cyclic GMP-AMP synthase (cGAS) binding to DNA and has 2.5-fold higher affinity to IFI16 than that of siRNA without the Motif. We further confirm that Motif siRNA potently suppresses HSV-1 virus-mediated IFNs and inflammatory cytokines, such as IFNL1, IFNB and TNFA, in human primary immature dendritic cells. Collectively, these findings may shed light on a novel function of siRNA with the unique 5-nt Motif as a quencher of innate immunity and facilitate the development of potential therapeutics to regulate innate immune cascades.
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siRNA containing a unique 5-Nucleotide Motif acts as a quencher of IFI16-mediated innate immune response
bioRxiv, 2019Co-Authors: Jun Yang, Xiaojun Hu, Tomozumi Imamichi, Qian ChenAbstract:We previously reported that small interfering RNA (siRNA) enhances DNA or DNA virus mediated-interferon (IFN)-λ1 induction through retinoic acid-inducible gene I (RIG-I) and interferon gamma-inducible protein 16 (IFI16) crosstalk-signalling pathway. Here we provide further evidence of a new role for siRNA. siRNA containing a 5-Nucleotide (nt) Motif sequence suppresses DNA-mediated IFNs and inflammatory cytokines. We determined that Motif siRNA inhibits the induction when the Motif is located at the 39 or 59-terminus of siRNA. Using THP1-Lucia ISG cells with various DNA stimulants, it is demonstrated that Motif siRNA inhibits DNA or DNA virus but not RNA virus-mediated signaling. Motif siRNA specifically interrupts IFI16 binding to DNA and has 2.5-fold higher affinity to IFI16 than that of siRNA without the Motif. Collectively, these findings may shed lights on a novel function of siRNA with the 5-nt Motif as a quencher of innate immunity and facilitate the development of potential therapeutics to treat diseases in which this pathway is dysregulated.
Jun Yang - One of the best experts on this subject based on the ideXlab platform.
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siRNA containing a unique 5-Nucleotide Motif acts as a quencher of IFI16-mediated innate immune response
Molecular Immunology, 2019Co-Authors: Jun Yang, Xiaojun Hu, Qian Chen, Tomozumi ImamichiAbstract:Abstract We previously reported that some small interfering RNA (siRNA) enhances DNA or DNA virus mediated-interferon (IFN)-λ1(a type III IFN) induction through the crosstalk between retinoic acid-inducible gene I (RIG-I) and interferon gamma-inducible protein 16 (IFI16) signalling pathway. Here we provide further evidence of a new role for siRNA. siRNA containing a 5-Nucleotide (nt) Motif sequence suppresses DNA-mediated not only type III IFNs, but also type I IFNs and inflammatory cytokines. We define that Motif siRNA inhibits the induction when the Motif is located at the 3′ or 5′-terminus of siRNA. Using THP1-Lucia ISG cells with various DNA stimulants, we reveal that Motif siRNA inhibits DNA or DNA virus but not RNA virus-mediated signalling. Motif siRNA specifically interrupts IFI16 but not cyclic GMP-AMP synthase (cGAS) binding to DNA and has 2.5-fold higher affinity to IFI16 than that of siRNA without the Motif. We further confirm that Motif siRNA potently suppresses HSV-1 virus-mediated IFNs and inflammatory cytokines, such as IFNL1, IFNB and TNFA, in human primary immature dendritic cells. Collectively, these findings may shed light on a novel function of siRNA with the unique 5-nt Motif as a quencher of innate immunity and facilitate the development of potential therapeutics to regulate innate immune cascades.
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siRNA containing a unique 5-Nucleotide Motif acts as a quencher of IFI16-mediated innate immune response
bioRxiv, 2019Co-Authors: Jun Yang, Xiaojun Hu, Tomozumi Imamichi, Qian ChenAbstract:We previously reported that small interfering RNA (siRNA) enhances DNA or DNA virus mediated-interferon (IFN)-λ1 induction through retinoic acid-inducible gene I (RIG-I) and interferon gamma-inducible protein 16 (IFI16) crosstalk-signalling pathway. Here we provide further evidence of a new role for siRNA. siRNA containing a 5-Nucleotide (nt) Motif sequence suppresses DNA-mediated IFNs and inflammatory cytokines. We determined that Motif siRNA inhibits the induction when the Motif is located at the 39 or 59-terminus of siRNA. Using THP1-Lucia ISG cells with various DNA stimulants, it is demonstrated that Motif siRNA inhibits DNA or DNA virus but not RNA virus-mediated signaling. Motif siRNA specifically interrupts IFI16 binding to DNA and has 2.5-fold higher affinity to IFI16 than that of siRNA without the Motif. Collectively, these findings may shed lights on a novel function of siRNA with the 5-nt Motif as a quencher of innate immunity and facilitate the development of potential therapeutics to treat diseases in which this pathway is dysregulated.
Christophe Carnoy - One of the best experts on this subject based on the ideXlab platform.
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the dif xer recombination systems in proteobacteria
PLOS ONE, 2009Co-Authors: Christophe Carnoy, Claude-alain H. RotenAbstract:In E. coli, 10 to 15% of growing bacteria produce dimeric chromosomes during DNA replication. These dimers are resolved by XerC and XerD, two tyrosine recombinases that target the 28-Nucleotide Motif (dif) associated with the chromosome's replication terminus. In streptococci and lactococci, an alternative system is composed of a unique, Xer-like recombinase (XerS) genetically linked to a dif-like Motif (difSL) located at the replication terminus. Preliminary observations have suggested that the dif/Xer system is commonly found in bacteria with circular chromosomes but that assumption has not been confirmed in an exhaustive analysis. The aim of the present study was to extensively characterize the dif/Xer system in the proteobacteria, since this taxon accounts for the majority of genomes sequenced to date. To that end, we analyzed 234 chromosomes from 156 proteobacterial species and showed that most species (87.8%) harbor XerC and XerD-like recombinases and a dif-related sequence which (i) is located in non-coding sequences, (ii) is close to the replication terminus (as defined by the cumulative GC skew) (iii) has a palindromic structure, (iv) is encoded by a low G+C content and (v) contains a highly conserved XerD binding site. However, not all proteobacteria display this dif/XerCD system. Indeed, a sub-group of pathogenic e-proteobacteria (including Helicobacter sp and Campylobacter sp) harbors a different recombination system, composed of a single recombinase (XerH) which is phylogenetically distinct from the other Xer recombinases and a Motif (difH) sharing homologies with difSL. Furthermore, no homologs to dif or Xer recombinases could be detected in small endosymbiont genomes or in certain bacteria with larger chromosomes like the Legionellales. This raises the question of the presence of other chromosomal deconcatenation systems in these species. Our study highlights the complexity of dif/Xer recombinase systems in proteobacteria and paves the way for systematic detection of these components in prokaryotes.
Elisha D.o. Roberson - One of the best experts on this subject based on the ideXlab platform.
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Motif scraper: a cross-platform, open-source tool for identifying degenerate Nucleotide Motif matches in FASTA files.
Bioinformatics (Oxford England), 2018Co-Authors: Elisha D.o. RobersonAbstract:Summary Many genomic features are defined not by exact sequence matches, but by degenerate Nucleotide Motifs that represent multiple compatible matches. While there are databases cataloging genomic features, such as the location of transcription factor Motifs, for commonly used model species, identifying the locations of novel Motifs, known Motifs in non-model genomes, or known Motifs in personal whole-genomes is difficult. I designed Motif scraper to overcome this limitation, allowing for efficient, multiprocessor Motif searches in any FASTA file. Availability and implementation The Motif scraper package (MIT license) is available via PyPI, and the Python source is available on GitHub at https://github.com/RobersonLab/Motif_scraper.
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Motif Scraper: A cross-platform, open-source tool for identifying degenerate Nucleotide Motif matches in FASTA files
bioRxiv, 2018Co-Authors: Elisha D.o. RobersonAbstract:Many genomic features are defined not by exact sequence matches, but by degenerate Nucleotide Motifs that represent multiple compatible matches. While there are databases cataloging genomic features, such as the location of transcription factor Motifs, for commonly used model species, identifying the locations of novel Motifs, known Motifs in non-model genomes, or known Motifs in personal whole-genomes is difficult. I designed Motif scraper to overcome this limitation, allowing for efficient, multiprocessor Motif searches in any FASTA file.
Qian Chen - One of the best experts on this subject based on the ideXlab platform.
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siRNA containing a unique 5-Nucleotide Motif acts as a quencher of IFI16-mediated innate immune response
Molecular Immunology, 2019Co-Authors: Jun Yang, Xiaojun Hu, Qian Chen, Tomozumi ImamichiAbstract:Abstract We previously reported that some small interfering RNA (siRNA) enhances DNA or DNA virus mediated-interferon (IFN)-λ1(a type III IFN) induction through the crosstalk between retinoic acid-inducible gene I (RIG-I) and interferon gamma-inducible protein 16 (IFI16) signalling pathway. Here we provide further evidence of a new role for siRNA. siRNA containing a 5-Nucleotide (nt) Motif sequence suppresses DNA-mediated not only type III IFNs, but also type I IFNs and inflammatory cytokines. We define that Motif siRNA inhibits the induction when the Motif is located at the 3′ or 5′-terminus of siRNA. Using THP1-Lucia ISG cells with various DNA stimulants, we reveal that Motif siRNA inhibits DNA or DNA virus but not RNA virus-mediated signalling. Motif siRNA specifically interrupts IFI16 but not cyclic GMP-AMP synthase (cGAS) binding to DNA and has 2.5-fold higher affinity to IFI16 than that of siRNA without the Motif. We further confirm that Motif siRNA potently suppresses HSV-1 virus-mediated IFNs and inflammatory cytokines, such as IFNL1, IFNB and TNFA, in human primary immature dendritic cells. Collectively, these findings may shed light on a novel function of siRNA with the unique 5-nt Motif as a quencher of innate immunity and facilitate the development of potential therapeutics to regulate innate immune cascades.
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siRNA containing a unique 5-Nucleotide Motif acts as a quencher of IFI16-mediated innate immune response
bioRxiv, 2019Co-Authors: Jun Yang, Xiaojun Hu, Tomozumi Imamichi, Qian ChenAbstract:We previously reported that small interfering RNA (siRNA) enhances DNA or DNA virus mediated-interferon (IFN)-λ1 induction through retinoic acid-inducible gene I (RIG-I) and interferon gamma-inducible protein 16 (IFI16) crosstalk-signalling pathway. Here we provide further evidence of a new role for siRNA. siRNA containing a 5-Nucleotide (nt) Motif sequence suppresses DNA-mediated IFNs and inflammatory cytokines. We determined that Motif siRNA inhibits the induction when the Motif is located at the 39 or 59-terminus of siRNA. Using THP1-Lucia ISG cells with various DNA stimulants, it is demonstrated that Motif siRNA inhibits DNA or DNA virus but not RNA virus-mediated signaling. Motif siRNA specifically interrupts IFI16 binding to DNA and has 2.5-fold higher affinity to IFI16 than that of siRNA without the Motif. Collectively, these findings may shed lights on a novel function of siRNA with the 5-nt Motif as a quencher of innate immunity and facilitate the development of potential therapeutics to treat diseases in which this pathway is dysregulated.
