Mapping R-Loops and RNA:DNA Hybrids with S9.6-Based Immunoprecipitation Methods

10.3791/62455 ◽  
2021 ◽  
Author(s):  
Lionel A. Sanz ◽  
Daisy Castillo-Guzman ◽  
Frédéric Chédin
Keyword(s):  
Rna:Dna Hybrids

scholarly journals Hydroxychloroquine modulates immunological pathways activated by RNA:DNA hybrids in Aicardi–Goutières syndrome patients carrying RNASEH2 mutations

2021 ◽  
Author(s):  
Jessica Garau ◽  
Daisy Sproviero ◽  
Francesca Dragoni ◽  
Elisa Piscianz ◽  
Carolina Santonicola ◽  
...  
Keyword(s):  
Rna:Dna Hybrids

scholarly journals Evolutionary History and Activity of RNase H1-Like Proteins in Arabidopsis thaliana

2020 ◽  
Vol 61 (6) ◽  
pp. 1107-1119
Author(s):  
Jan Kuciński ◽  
Sebastian Chamera ◽  
Aleksandra Kmera ◽  
M Jordan Rowley ◽  
Sho Fujii ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Embryonic Development ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Normal Growth ◽  
Plastid Dna ◽  
Growth Conditions ◽  
Replicative Stress ◽  
The Common ◽  
Rna:Dna Hybrids

Abstract RNase H1 is an endonuclease specific toward the RNA strand of RNA:DNA hybrids. Members of this protein family are present in most living organisms and are essential for removing RNA that base pairs with DNA. It prevents detrimental effects of RNA:DNA hybrids and is involved in several biological processes. Arabidopsis thaliana has been previously shown to contain three genes encoding RNase H1 proteins that localize to three distinct cellular compartments. We show that these genes originate from two gene duplication events. One occurred in the common ancestor of dicots and produced nuclear and organellar RNase H1 paralogs. Second duplication occurred in the common ancestor of Brassicaceae and produced mitochondrial- and plastid-localized proteins. These proteins have the canonical RNase H1 activity, which requires at least four ribonucleotides for endonucleolytic digestion. Analysis of mutants in the RNase H1 genes revealed that the nuclear RNH1A and mitochondrial RNH1B are dispensable for development under normal growth conditions. However, the presence of at least one organellar RNase H1 (RNH1B or RNH1C) is required for embryonic development. The plastid-localized RNH1C affects plastid DNA copy number and sensitivity to replicative stress. Our results present the evolutionary history of RNH1 proteins in A. thaliana, demonstrate their canonical RNase H1 activity and indicate their role in early embryonic development.

The dark side of RNA:DNA hybrids

2020 ◽  
Vol 784 ◽  
pp. 108300 ◽  
Author(s):  
Alessandra Brambati ◽  
Luca Zardoni ◽  
Eleonora Nardini ◽  
Achille Pellicioli ◽  
Giordano Liberi
Keyword(s):  
Dark Side ◽  
Rna:Dna Hybrids

A map of cytoplasmic RNA transcripts from lytic adenovirus type 2, determined by electron microscopy of RNA:DNA hybrids

Cell ◽  
1977 ◽  
Vol 11 (4) ◽  
pp. 819-836 ◽  
Author(s):  
Louise T. Chow ◽  
James M. Roberts ◽  
James B. Lewis ◽  
Thomas R. Broker
Keyword(s):  
Electron Microscopy ◽  
Adenovirus Type ◽  
Rna Transcripts ◽  
Cytoplasmic Rna ◽  
Rna:Dna Hybrids ◽  
Adenovirus Type 2

Detection of sickle-cell mutation by electrophoresis of partial RNA:DNA hybrids following solution hybridization

Gene ◽  
1985 ◽  
Vol 39 (1) ◽  
pp. 77-83 ◽  
Author(s):  
Frederick S. Jones ◽  
Jacob I. Grimberg ◽  
Stuart G. Fischer ◽  
John P. Ford
Keyword(s):  
Sickle Cell ◽  
Cell Mutation ◽  
Rna:Dna Hybrids

scholarly journals Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system

2015 ◽  
Vol 112 (18) ◽  
pp. 5779-5784 ◽  
Author(s):  
Ruth Stuckey ◽  
Néstor García-Rodríguez ◽  
Andrés Aguilera ◽  
Ralf Erik Wellinger
Keyword(s):  
Genome Duplication ◽  
S Phase ◽  
Rna Polymerase I ◽  
Replication Origins ◽  
Replication Process ◽  
Number Variation ◽  
Independent Replication ◽  
Rna:Dna Hybrids ◽  
Polymerase I ◽  
Eukaryotic Genomes

DNA replication initiates at defined replication origins along eukaryotic chromosomes, ensuring complete genome duplication within a single S-phase. A key feature of replication origins is their ability to control the onset of DNA synthesis mediated by DNA polymerase-α and its intrinsic RNA primase activity. Here, we describe a novel origin-independent replication process that is mediated by transcription. RNA polymerase I transcription constraints lead to persistent RNA:DNA hybrids (R-loops) that prime replication in the ribosomal DNA locus. Our results suggest that eukaryotic genomes have developed tools to prevent R-loop–mediated replication events that potentially contribute to copy number variation, particularly relevant to carcinogenesis.

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