Chapter title |
Detection and Characterization of R Loop Structures
|
---|---|
Chapter number | 13 |
Book title |
Promoter Associated RNA
|
Published in |
Methods in molecular biology, March 2017
|
DOI | 10.1007/978-1-4939-6716-2_13 |
Pubmed ID | |
Book ISBNs |
978-1-4939-6714-8, 978-1-4939-6716-2
|
Authors |
Raquel Boque-Sastre, Marta Soler, Sonia Guil |
Editors |
Sara Napoli |
Abstract |
R loops are special three stranded nucleic acid structures that comprise a nascent RNA hybridized with the DNA template strand, leaving a non-template DNA single-stranded. More specifically, R loops form in vivo as G-rich RNA transcripts invade the DNA duplex and anneal to the template strand to generate an RNA:DNA hybrid, leaving the non-template, G-rich DNA strand in a largely single-stranded conformation (Aguilera and Garcia-Muse, Mol Cell 46:115-124, 2012).DNA-RNA hybrids are a natural occurrence within eukaryotic cells, with levels of these hybrids increasing at sites with high transcriptional activity, such as during transcription initiation, repression, and elongation. RNA-DNA hybrids influence genomic instability, and growing evidence points to an important role for R loops in active gene expression regulation (Ginno et al., Mol Cell 45, 814-825, 2012; Sun et al., Science 340: 619-621, 2013; Bhatia et al., Nature 511, 362-365, 2014). Analysis of the occurrence of such structures is therefore of increasing relevance and herein we describe methods for the in vivo and in vitro identification and characterization of R loops in mammalian systems.R loops (DNA:RNA hybrids and the associated single-stranded DNA) have been traditionally associated with threats to genome integrity, making some regions of the genome more prone to DNA-damaging and mutagenic agents. Initially considered to be rare byproducts of transcription, over the last decade accumulating evidence has pointed to a new view in which R loops form more frequently than previously thought. The R loop field has become an increasingly expanded area of research, placing these structures as a major threat to genome stability but also as potential regulators of gene expression. Special interest has arisen as they have also been linked to a variety of diseases, including neurological disorders and cancer, positioning them as potential therapeutic targets [5]. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 48 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 12 | 25% |
Student > Ph. D. Student | 8 | 17% |
Student > Postgraduate | 5 | 10% |
Student > Master | 4 | 8% |
Student > Bachelor | 3 | 6% |
Other | 7 | 15% |
Unknown | 9 | 19% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 33 | 69% |
Agricultural and Biological Sciences | 2 | 4% |
Immunology and Microbiology | 1 | 2% |
Chemistry | 1 | 2% |
Materials Science | 1 | 2% |
Other | 0 | 0% |
Unknown | 10 | 21% |