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Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA

by Storici, Francesca , Hesselberth, Jay R , Balachander, Sathya , Koh, Kyung Duk

in 45/23 / 631/1647/2217 / 631/208/176 / 631/208/212 / 631/337/1427 / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical Engineering/Biotechnology / Chromosome mapping / Deoxyribonucleic acid / DNA / DNA Replication / DNA, Fungal - genetics / DNA, Mitochondrial - genetics / GC Rich Sequence / Genetic Techniques / Genome, Fungal / Genomes / Genomics / High-Throughput Nucleotide Sequencing - methods / Life Sciences / Methods / Mitochondria / Mitochondrial DNA / Properties / Proteomics / Ribonucleotides / Ribonucleotides - analysis / Ribonucleotides - genetics / RNA sequencing / Saccharomyces cerevisiae / Saccharomyces cerevisiae - genetics / Uracil-DNA Glycosidase - genetics / Uracil-DNA Glycosidase - metabolism / Yeasts

2015

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Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA

by Storici, Francesca , Hesselberth, Jay R , Balachander, Sathya , Koh, Kyung Duk

2015

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Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA

by Storici, Francesca , Hesselberth, Jay R , Balachander, Sathya , Koh, Kyung Duk

2015

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Journal Article

Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA

Storici, Francesca,

Hesselberth, Jay R,

Balachander, Sathya,

Koh, Kyung Duk

2015

Overview

Ribose-seq allows ribose nucleotide (rNMP) incorporation to be detected genome-wide in DNA at single-base resolution and is demonstrated on budding yeast. Abundant ribonucleotide incorporation in DNA during replication and repair has profound consequences for genome stability, but the global distribution of ribonucleotide incorporation is unknown. We developed ribose-seq, a method for capturing unique products generated by alkaline cleavage of DNA at embedded ribonucleotides. High-throughput sequencing of these fragments in DNA from the yeast Saccharomyces cerevisiae revealed widespread ribonucleotide distribution, with a strong preference for cytidine and guanosine, and identified hotspots of ribonucleotide incorporation in nuclear and mitochondrial DNA. Ribonucleotides were primarily incorporated on the newly synthesized leading strand of nuclear DNA and were present upstream of (G+C)-rich tracts in the mitochondrial genome. Ribose-seq is a powerful tool for the systematic profiling of ribonucleotide incorporation in genomic DNA.

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Publisher

Nature Publishing Group US,Nature Publishing Group

Subject

/ Biological Microscopy