Topology of RNA:DNA Hybrids and R-Loops in Yeast.

DNA / chemistry DNA Replication R-Loop Structures RNA / chemistry Saccharomyces cerevisiae / genetics
DRIP-chip R-loop RNA:DNA hybrid S9.6 antibody

Journal

Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969

Informations de publication

Date de publication:
2022
Historique:
entrez: 15 6 2022
pubmed: 16 6 2022
medline: 18 6 2022
Statut: ppublish

Résumé

RNA:DNA hybrids are generated naturally behind the elongating RNA polymerase as a transcriptional intermediate. However, prolonged persistence of these structures challenges the integrity of the genome by creating R-loops and by interfering with DNA replication and other chromatin related processes. Precise mapping and characterization of their distribution across the genome has been a major challenge to understand the genesis of RNA:DNA hybrids and their conversion into genotoxic intermediates. Here we provide the detailed protocol for mapping RNA:DNA hybrid across the Saccharomyces cerevisiae genome.

Identifiants

DOI: 10.1007/978-1-0716-2477-7_21 PMID: 35704201
pubmed: 35704201
doi: 10.1007/978-1-0716-2477-7_21
doi:

Substances chimiques

RNA 63231-63-0
DNA 9007-49-2

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

317-328

Informations de copyright

© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Références

Duquette ML et al (2004) Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes Dev 18(13):1618–1629
doi: 10.1101/gad.1200804
Roy D, Lieber MR (2009) G clustering is important for the initiation of transcription-induced R-loops in vitro, whereas high G density without clustering is sufficient thereafter. Mol Cell Biol 29(11):3124–3133
doi: 10.1128/MCB.00139-09
Aguilera A, Garcia-Muse T (2012) R loops: from transcription byproducts to threats to genome stability. Mol Cell 46(2):115–124
doi: 10.1016/j.molcel.2012.04.009
Crossley MP, Bocek M, Cimprich KA (2019) R-loops as cellular regulators and genomic threats. Mol Cell 73(3):398–411
doi: 10.1016/j.molcel.2019.01.024
Achar YJ et al (2020) Negative supercoil at gene boundaries modulates gene topology. Nature 577(7792):701–705
doi: 10.1038/s41586-020-1934-4
Boguslawski SJ et al (1986) Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids. J Immunol Methods 89(1):123–130
doi: 10.1016/0022-1759(86)90040-2
Chan YA et al (2014) Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip. PLoS Genet 10(4):e1004288
doi: 10.1371/journal.pgen.1004288
Bermejo R et al (2009) ChIP-on-chip analysis of DNA topoisomerases. Methods Mol Biol 582:103–118
doi: 10.1007/978-1-60761-340-4_9
Droit A, Cheung C, Gottardo R (2010) rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments. Bioinformatics 26(5):678–679
doi: 10.1093/bioinformatics/btq023
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841–842
doi: 10.1093/bioinformatics/btq033

Auteurs

Yathish Jagadheesh Achar (YJ)

IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy. yathish@cdfd.org.in.
Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India. yathish@cdfd.org.in.

Marco Foiani (M)

IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy.
Università degli Studi di Milano, Milan, Italy.

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Classifications MeSH

questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Topology of RNA:DNA Hybrids and R-Loops in Yeast.
questionsmedicales.fr › Phénomènes génétiques › Réplication de l'ADN › Topology of RNA:DNA Hybrids and R-Loops in Yeast.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Structures en boucle R › Topology of RNA:DNA Hybrids and R-Loops in Yeast.
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › Topology of RNA:DNA Hybrids and R-Loops in Yeast.
questionsmedicales.fr › Eucaryotes › Champignons › Levures › Saccharomyces › Saccharomyces cerevisiae › Topology of RNA:DNA Hybrids and R-Loops in Yeast.