Genome mapping of RNA‒DNA hybrids in Escherichia coli

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Abstract

We have mapped RNA‒DNA hybrids in the prokaryotic genome for the first time. Using the S9.6 antibody immunoprecipitation method (S9.6-DRIP) followed by whole-genome sequencing, we identified 219 unique peaks of RNA‒DNA hybrids in the genome of Escherichia coli TOP10. These peaks corresponded to 219 different genes and were predominantly distributed in the coding regions of the genome (88.12%). Analysis of individual genes containing RNA‒DNA hybrids revealed that they encode enzymes involved in important energy and metabolic processes in prokaryotes, such as lipoic acid synthesis.

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About the authors

K. Y. Oleynikova

FRC Fundamentals of Biotechnology of the Russian Academy of Sciences

Email: nzhigalova@gmail.com

K.G. Skryabin Institute of Bioengineering

Russian Federation, Moscow, 119071

A. S. Ruzov

FRC Fundamentals of Biotechnology of the Russian Academy of Sciences

Email: nzhigalova@gmail.com

K.G. Skryabin Institute of Bioengineering

Russian Federation, Moscow, 119071

N. A. Zhigalova

FRC Fundamentals of Biotechnology of the Russian Academy of Sciences

Author for correspondence.
Email: nzhigalova@gmail.com

K.G. Skryabin Institute of Bioengineering

Russian Federation, Moscow, 119071

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2. Fig. a – Diagram demonstrating the distribution of consensus peaks for S9.6 samples by genomic components; b – profile plot showing the saturation of DRIP-seq reads by genomic regions containing genes. In this case, genes were defined as genomic regions including 300 nucleotides (promoter region) before the transcription start signal (TSS), the gene body and 300 nucleotides after the transcription termination signal (TTS), (u – saturation units); c – shows the distribution of DRIP read densities for a representative region of the bacterial genome with coordinates: 660000‒665000, which well reflects the signals for all samples of the experiment.

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